Research Topic

Organization, Dynamics, and Life

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Life phenomena arise from collections of interacting entities that, by interacting, provoke changes in the biological system. Current methodologies in natural sciences, describe phenomena by considering interacting components in definite classes: particles, fields, waves, substances, molecules, cells, ...

Life phenomena arise from collections of interacting entities that, by interacting, provoke changes in the biological system. Current methodologies in natural sciences, describe phenomena by considering interacting components in definite classes: particles, fields, waves, substances, molecules, cells, individuals, populations, species etc. Each class reflects characteristics we consider important ignoring those we think irrelevant. They constrain which aspects make sense, can be observed and studied, and act as perspectives to observe, model and understand a phenomenon. Properties like pressure, mass, temperature, tension, stability and organisation appear as by-products of dynamics, continuity, or topology. There is no room in theories derived from these perspectives to handle properties that result from long-lasting but mutable interactions such as bio-chemical bonds. Molecules are formally treated as immutable particles or substances.

Molecular structure/conformation and their intracellular environment give rise to chemical affinity and activity influencing which molecules interact, which do not interact and affecting reaction rates. Affinity is architectural and doesn’t result from dynamics. Molecules are comprised of atoms and affinity depends on highly specific organisations. Concepts like chains, structures, subdomains and conformational states are relevant when describing chemical behaviour. Nevertheless, current formalisms do not allow for considering organisations as interacting entities nor for inferring affinities entailed by organisations.

Organisation permeates living systems at all scales. It refers to the relative position components adopt relative to one another and
affects interactions and biological outcome, as in molecular recombination, foraging, infection and mitosis. Biological function is literally an emergent property arising from organisations interacting at different scales. Cells are organisations of modules and compartments, while metabolic cycles are organisations of biochemical processes.

Biological organisation arises from constraining interactions and components to work together in modular units. Different organisations emerge from the same constituents. Making the role of organisation explicit is fundamental to understand living phenomena. Re-organisations in space and time do affect propensities in behaviour due to vibrations, docking, and conformational changes. Moreover, appropriate environments must be present to enable biological interactions. The idea of considering interacting organisations and processes, as well as the proper organisation of interactions emerges naturally from this perspective.

Biochemical networks and trophic webs are simple organisations. Several models and explanations have been proposed for their organisation, allowing for a deeper investigation about their role in life. Modelling and reasoning about organisations are often intertwined with information, complexity and computer science concepts. Scientists with different backgrounds have endeavoured to explain organisation or used organisation to explain the living. Organisation, however, remains a poorly elaborated concept, used in an ancillary manner when discussing the phenomena of life.

The purpose of this Research Topic is threefold: (1) investigate organisation as a guiding principle to observe, model and explain life; (2) explain the nature of biological organisation and function; and (3) present a perspective that enhances how we describe and understand life. We welcome investigations at all biological scales — from sub-cellular to environmental – and from a theoretical, computational, data-driven or experimental perspective.


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