Primal awareness, evolutionary restriction, life and the origin of quantum mechanics.

We consider resemblances between humans and other species, without adopting categorical positions of either anthropomorphism or anti-anthropomorphism. Our target in doing so is to present a basis for the suggestion of a common ancestor for the similar or differing capabilities exhibited by different species. We propose that individual species exhibit a species-specific selection within what we describe as a universally available 'Basic Capacity to Interact with the Environment' (BCIE). We justify this proposition in terms of the ubiquitous presence at all organizational levels of the Universe of a primal awareness - a precursor of Nature. On disassembling natural organic systems - through neurons, biochemistry … down to quantum mechanics, we note that in its suggested position coupling input-to-output in quantum mechanical operations, primal awareness would be the precursor of quantum mechanics itself. We relate ubiquitous primal awareness to the ideas of David Bohm and Charles Peirce. We point out that genetic Evolution not only provides the basis for the implementation of many capabilities through our 'Basic Capacity to Interact with the Environment', but equally excludes numerous others. This then could explain why different species' Evolution fixes their available/unavailable capabilities. Quantum mechanical superposition/coherence/entanglement are related to our universal primal awareness, in its sense as a ubiquitous precursor. We point out that life is dependent on the classical simulation of quantum mechanics.

The local-global relationship of nature.

In the light of possible advance in the elucidation of emergence in natural systems we address the likelihood of an overriding relationship between the local and the global in Nature. We consider the possible views of an abstract conglomeration of entities, and whether a global representation can be established. This leads to a consideration of the problem in natural contexts to establish a relationship between local and global properties. We describe the application of a model-hierarchical representation to a biological cell, and its implications in terms of subjective and objective viewpoints. We conclude by stating the concluded relationship between local and global properties in Nature, in that control is exercised not only from local-to-global, but also from global-to-local.

Origin of the temporal stability control of living system nonequilibrium.

Following Ervin Bauer we accept that a living system can be characterized by its stable nonequilibrium. We represent such a system by a model hierarchy and relate system stability to computational delays across the hierarchy. For natural computation across the system assembly we advocate chaotic computation, and evaluate computational delay at the different organizational levels of the hierarchy. We compute inter-elemental access speed for the atomic and cell levels, and conclude that cell-related speed is 1000-10,000 times that of the atom level, confirming that on moving from the system-as-itself level towards the system-as-atoms level overall level access speed reduces. We conclude that Bauer's living system description as a stable nonequilibrium is justified.

Entropy is better related to unification than to order.

There are difficulties related to the classical establishment of entropy. It is conventionally viewed as the inverse of order in a system, or more precisely as a quantification of the number of possible systemic microstate reorganisations. This should attribute the related energy to a spectrum of possibilities, from the conventionally 'expected order at one end to a different unexpected order at the other, with disorder between the two', rather than the conventional 'order at one end to disorder at the other'. We propose that the resolution of this dichotomy lies in relating entropy to system unification, in place of simplistic order, which in any case is unfathomable in a complex organisationally multi-levelled organism. We conclude by questioning the entropic place of the brain in the Universe.

Chaos, complexity and computation in the evolution of biological systems.

Chaos, complexity and computation are especially important concepts with respect to both the Evolution of biological systems and the evolution of the Universe. We consider each of these five entities separately, and then view their combination in an overall consideration of both evolution and Evolution. The concept of computation can be directly derived from processes characteristic of the Evolution of biology or the evolution of the Universe, rather than presumed from our own mathematical ideas. We advocate the inclusion of meaning in science's deliberations, and support this by insisting that physically embodied abstractions should be considered part concrete in character. Combination of our initial five conceptual entities indicates that biological Evolution follows the same developmental criteria as the evolution of the Universe, albeit with an intermediate change in strategy. We conclude that evolutionarily derived computation is the prime driver of evolution/Evolutions' implications.

Computation in biological systems as a quantum mechanical simulation.

Our initial premise is that computation as we know it is formally derived from our bodies' internal processing, via our neural processors. Going backwards in time, our bodies' internal processing is in turn derived from wider Nature's own style of processing, which in turn is a rendition of the Universe's processing following the Big Bang. Computation is described as consisting of two intimately connected parts: comparative processing and conclusive processing. Our examination of post-Big Bang processing, biological processing, neural processing and human thinking supports our initial premise and the conclusion that computation is the motor for evolutionary emergence across the entire timescale of the Universe.

An approach to the plant body: Assessing concrete and abstract aspects.

The paper aims at proposing a representation of plants as individuals. The first section selects the population of plants to which this study is addressed. The second section describes the effective architecture of plants as modular systems with fixed and mobile elements, in other words, plants and their extensions. The third section presents how plants integrate the fixed and mobile modules into functional units through three areas of particular relevance to plant growth and development: nutrition, defence and pollination. Based on the tangible elements introduced in the previous sections, the fourth section presents the main issue of the proposal which is not apparent at first glance, namely, the local-global relationship in plants' architecture that determines their individuality as organisms. Finally, in the conclusion, we issue the challenge of developing a collective presentation of plants which satisfies their complementary dimension.

The necessity of hierarchy for living systems.

We present a short critique of living systems and of hierarchy, and then present model hierarchy as the parent of other less elaborate schemes. Model hierarchy consists of a number of organizational levels, each a scaled model of the entire system under consideration. Cross-hierarchy coherence is paramount. The model-hierarchical representation of an organism splits into two partial hierarchies, one of the model levels, the other of the intervening complex regions. We propose that model hierarchy is the most fundamental aspect of living systems, in that it permits the operation of all other characteristics of life. We present a computational analogue to model hierarchy - AQUARIUM - and integrate the two representations. Neural processing suffers from an omission in its formulation, and we link this processing duality to classical simulation of quantum processes. We describe the way in which inter-organizational transit may be accomplished by means of a generic form of quantum error correction. We conclude that model hierarchy is fundamental to the existence of living systems, as is the classical simulation of quantum processes.

Representing life: A natural philosophical project.

We address multi-levelled organization as a vital aspect of any characterization of Nature, and propose that a model-hierarchical description is fitting for a Natural Philosophical point of view. An important aspect is that the different organizational levels in a model hierarchy are partially isolated and autonomous, partially communicating across the entire scale assembly. Of particular interest are the complex interfaces between levels, and the manner in which these may be transited by a generic form of quantum error correction. An entire hierarchy decomposes into two partial hierarchies, one of the model levels, one of the complex interfaces. These are both approximately modelled, both internally and externally, as a duality of hyperscales, which ultimately integrate to give a singular metascalar identity: the duality we propose is not that of Descartes, but is a natural outcome of multi-levelled modelling. We note that a Natural Philosophical view of Nature must include a sense of meaning, related to Aristotle's fourth cause, and that this makes a clear difference from conventional Scientific practice. Life can be well represented by this hierarchical snapshot of its structure, although a more comprehensive view must invoke the characteristics of living, and not just life per se.

The living organism: Strengthening the basis.

In spite of the considerable amount of literature dedicated to the living organism, it retains its mysteries. One of the most discussed aspects nowadays is whether the term "cognition" can be attributed to all classes of organisms, or whether it only refers to a metaphoric use of one human reality. Our approach consists of retaining the term "cognition" and making it a technical term, in order to propose a generic model. In this way, cognition becomes what finally characterises an organism as an autonomous agent. This perspective eliminates some misplaced questions, and helps to reframe old ones. The cognitive dimension can be apprehended indirectly only through its appearances. These direct us towards a modular model of cognition and orientate research towards the clarification of specific modules for each class of organisms.

Toward bridging the gap between life and physics.

Examination of the scale properties of living organisms and the electronic configuration of crystalline structures suggests that related modeling may be used for both. This paper comments on individual and common properties of the two systems and draws a comparison between them. Both exhibit multiple 'scales' separated by complex or forbidden regions and a global 'overview' of their scale properties. We conclude that the analogy may provide a fruitful route toward extension of the modeling of both living organisms and electronic materials, by permitting bootstrapping cross-modeling between them.

Re-mapping Robert Rosen's (M,R)-systems.

The central concern of this paper is to re-evaluate Rosen's replicating (M,R)-systems, presented in his book 'Life Itself ', where M and R signify metabolism and repair, respectively. We look anew at Rosen's model of an organism in the light of extensive research into natural hierarchical systems, and the paper presents conclusions drawn from a comparison between Rosen's relational model and that of a birational complementary natural hierarchy. We accept that Rosen's relational model provides a useful stepping stone to understanding the nature of life, but also suggest that it induces potentially digressive conclusions. We conclude that a binary segregation of relational assemblies into mechanisms and organisms is insufficient, and indicate how a threefold segregation throws new light on Rosen's model. An organism is not 'the complement of a mechanism': the complement of a mechanism is its ecosystem. An organism is the 'complex interface' between mechanism and ecosystem.