The universal principles of self-organization and the unity of Nature and knowledge


It is argued that diverse complex adaptive systems, such as proteins, cells, organisms, organizations, societies and ecosystems, all together constitute one developing, multiscale continuum-economy composed of interacting and interdependent adaptive organizational forms that co-exist and co-evolve at different spatiotemporal scales, forming a nested set of interdependent organizational hierarchies. When reconceptualized in equivalent terms of self-organizing adaptive networks of energy/matter/information exchanges, complex systems of different scales appear to exhibit universal scale-invariant patterns in their organization and dynamics, suggesting the self-similarity of spatiotemporal scales and fractal organization of the living matter continuum.

The self-organization of biomolecules into cells, cells into organisms and organisms into societies and ecosystems is presented here in terms of a universal scale-invariant organizational process driven by economy and assisted by memory and innovation. It is driven by economy as individual adaptive organizations compete and cooperate at every scale in their efforts to maximize the rate and efficiency of energy/matter/information extraction from their environments and the rate and efficiency of negative entropy production. Evolutionary memory, manifested as organizational structure balancing economic efficiency and adaptability, and innovation, manifested as stochastic generation of new organizational forms, facilitate economy-driven self-organization. Self-organization is proposed to be an ever-expanding process covering increasingly larger spatiotemporal scales through formation of interdependent organizational hierarchies. The process of self-organization blends Darwinian phases dominated by diversification, competition, and selection and organizational phases dominated by specialization, cooperation, and organization.

It is argued and illustrated that the self-similarity of spatiotemporal scales in the organization and dynamics of living matter can be exploited both for scientific discovery within specialized disciplines and the unification of individual sciences within one and the same conceptual framework of self-organization. This is achieved by 1) defining scale-invariant organizational concepts, patterns and measures; 2) reconceptualizing organizational phenomena of different scales in the same scale-invariant terms and 3) mapping the knowledge structures of different scales onto each other, using overlapping patterns for alignment, filling in missing parts, and re-structuring misaligned patterns on the assumption of spatiotemporal self-similarity of scales.

Keywords : self-organization; scale-invariant organization and dynamics; self-organizing fractal theory (SOFT); adaptation through organizational state transitions; innovation through stochasticity; structure as evolutionary memory; steady-state metastability; integration through moonlighting; inter-scale conceptual mapping; self-organization as cognition.

3 August 2007, Novato, CA



Descartes and Newton placed firm foundations for the emergence, development and success of modern sciences. The unsurpassed economic achievements of the Industrial Revolution ignited and fueled by Newtonian science have been matched by the increasing pressure of mechanistic instruction in professional training, education and in society at large. The mechanistic worldview and reductionism have rarely failed Western societies, economically speaking, and have eventually become unconscious operational defaults of the Western mind. We are compelled to interpret reality in mechanistic terms and to approach analysis of any phenomenon by taking it apart to ever-smaller pieces, studying pieces in isolation and deducing the underlying design. It is not surprising, therefore, that molecular and cell biology, where the greatest majority of studies are performed in the spirit of reverse engineering, came to be dominated by clockwork images of macromolecules, cells and organisms. "One of the acid tests of understanding an object is the ability to put it together from its component parts. Ultimately, molecular biologists will attempt to subject their understanding of cell structure and function to this sort of test by trying to synthesize a cell" (1).

Disconcertingly, even a cursory overview of accumulated research literature strongly suggests that familiar and appealing mechanistic concepts and interpretations have become manifestly inconsistent with experimental reality at all scales of biological organization, from macromolecules through sub-cellular organization and individual cells to whole organisms, thus suggesting a systemic crisis of the mechanistic paradigm and reductionism in life sciences (2-5) . The classico-mechanistic conceptualization, when applied to biological phenomena, appears to have evolved from an insufficient but convenient analogy to the mental block that precludes understanding and adequate modeling of living systems (5).

In the search for alternative conceptualizations of biological complexity, stochasticity as a general principle of differentiation and adaptation, and self-organization as a concept of emergence, were suggested as the core of an emerging interpretational framework promising to unite phenomena across different scales of biological organization, from molecules to societies (3, 6, 7). The conceptual framework of self-organization was used to rationalize and explain a variety of otherwise paradoxical experimental observations pertaining to molecular motors and protein translocation (4), sub-cellular organization (2, 6), stochasticity in gene expression, cell plasticity, organism development and other biological phenomena (3, 8, 9). Expanding the paradigm of self-organization, such concepts as evolutionary memory, bounded stochasticity and adaptive plasticity were recently introduced to resolve a contradiction between the inherent ambiguity of molecular recognition and the apparent specificity and order observed in intracellular signaling and metabolic conversions (7).

Unlike mechanistic interpretations, emerging concepts of self-organization appear to be consistent with experimental reality at all scales of biological organization and are universally meaningful whether one speaks about biomolecules, sub-cellular structures, cells, organisms or social and business organizations, and whether one considers phylogenetic or ontogenetic time scales. In other words, the concepts of self-organization appear to be scale-invariant, suggesting that they may reflect certain universal attributes common to diverse complex phenomena taking place at different spatiotemporal scales. The universality of organizational patterns across scales of biological complexity becomes especially apparent when complex phenomena/systems of different scales, such as proteins, cells, organisms, ecosystems, organizations, societies and economies, are reconceptualized in equivalent terms of self-organizing adaptive networks of energy/matter/information exchanges (10-14).

It is argued in this essay that the apparent self-similarity of scales in biological (broadly defined) systems is a consequence of the unity and fractality of living matter, which exists and evolves in reality as one dynamic multiscale organization/continuum of intelligence composed of the interdependent and mutually defining/morphing adaptive organizational forms of energy/matter/information exchanges manifested as biomolecules, cells, organisms, ecosystems, organizations, societies and so forth. It is only the culturally acquired habit of misconceptualizing living matter in mechanistic terms that makes biomolecules, cells, organisms, ecosystems, organizations and societies to appear to the reductionist mind of the human observer as if they were isolated, self-defined, standardized and interchangeable systems of the mechanistic type, designed for some purpose, i.e. as parts of the Machine.

It is suggested that the development and expansion of the continuum of living matter proceeds through the process of self-organization driven by economic competition and facilitated by memory and stochasticity/innovation. The economic competition between alternative organizational forms is resolved to the common benefit of surviving competitors through cooperation, specialization, organization and formation of self-affine organizational hierarchies.

The arguments and discussion presented are intentionally kept qualitative and descriptive. However, references are made to the quantitative frameworks that are in place to step in. Fractality is qualitatively defined as similarity of the spatial and/or temporal organizational patterns reproduced again and again at different scales of space and/or time. Fractality is presented and used as a form of symmetry, i.e. as the invariance of a pattern/form in relation to scaling.

It is demonstrated that scale invariance of the organizational patterns underlying complex adaptive phenomena of different scales can be exploited for scientific discovery by 1) reconceptualizing diverse complex phenomena in the same conceptual terms of self-organization, 2) mapping the specific knowledge structures developed within specialized disciplines onto each other and 3) filling in the gaps in the aligned knowledge structures and re-structuring misaligned parts on the assumption of spatiotemporal self-similarity of scales.

The reconceptualization of biological and other phenomena within the framework of self-organization is unavoidably contrasted with familiar textbook images of the same phenomena, which, for the most part, are products of the mechanistic interpretation of living matter and which reside in our unconscious as unquestioned and often unquestionable defaults and assumptions. As the conventional and habitual tend to acquire the quality of faith and relative independence from reality with time, the experimental evidence inconsistent with conventional mechanistic interpretations but supporting the conceptualization of biological and other phenomena in terms of self-organization is reviewed throughout the essay.

Because, as it is argued further, economic development and competition are at the heart of all self-organizational phenomena, let us begin our inquiry into the nature and causes of self-organization with a discussion of an unconventional theory dealing with the emergence, organization and evolution of the economy at the cellular scale known as cellular metabolism.


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