The INBIOSA project brings together a group of experts across many disciplines who believe that science requires a revolutionary transformative step in order to address many of the vexing challenges presented by the world. It is INBIOSA’s purpose to enable the focused collaboration of an interdisciplinary community of original thinkers. This paper sets out the case for support for this effort. The focus of the transformative research program proposal is biology-centric. We admit that biology to date has been more fact-oriented (...) and less theoretical than physics. However, the key leverageable idea is that careful extension of the science of living systems can be more effectively applied to some of our most vexing modern problems than the prevailing scheme, derived from abstractions in physics. While these have some universal application and demonstrate computational advantages, they are not theoretically mandated for the living. A new set of mathematical abstractions derived from biology can now be similarly extended. This is made possible by leveraging new formal tools to understand abstraction and enable computability. [The latter has a much expanded meaning in our context from the one known and used in computer science and biology today, that is "by rote algorithmic means", since it is not known if a living system is computable in this sense (Mossio et al., 2009).] Two major challenges constitute the effort. The first challenge is to design an original general system of abstractions within the biological domain. The initial issue is descriptive leading to the explanatory. There has not yet been a serious formal examination of the abstractions of the biological domain. What is used today is an amalgam; much is inherited from physics (via the bridging abstractions of chemistry) and there are many new abstractions from advances in mathematics (incentivized by the need for more capable computational analyses). Interspersed are abstractions, concepts and underlying assumptions “native” to biology and distinct from the mechanical language of physics and computation as we know them. A pressing agenda should be to single out the most concrete and at the same time the most fundamental process-units in biology and to recruit them into the descriptive domain. Therefore, the first challenge is to build a coherent formal system of abstractions and operations that is truly native to living systems. Nothing will be thrown away, but many common methods will be philosophically recast, just as in physics relativity subsumed and reinterpreted Newtonian mechanics. -/- This step is required because we need a comprehensible, formal system to apply in many domains. Emphasis should be placed on the distinction between multi-perspective analysis and synthesis and on what could be the basic terms or tools needed. The second challenge is relatively simple: the actual application of this set of biology-centric ways and means to cross-disciplinary problems. In its early stages, this will seem to be a “new science”. This White Paper sets out the case of continuing support of Information and Communication Technology (ICT) for transformative research in biology and information processing centered on paradigm changes in the epistemological, ontological, mathematical and computational bases of the science of living systems. Today, curiously, living systems cannot be said to be anything more than dissipative structures organized internally by genetic information. There is not anything substantially different from abiotic systems other than the empirical nature of their robustness. We believe that there are other new and unique properties and patterns comprehensible at this bio-logical level. The report lays out a fundamental set of approaches to articulate these properties and patterns, and is composed as follows. -/- Sections 1 through 4 (preamble, introduction, motivation and major biomathematical problems) are incipient. Section 5 describes the issues affecting Integral Biomathics and Section 6 -- the aspects of the Grand Challenge we face with this project. Section 7 contemplates the effort to formalize a General Theory of Living Systems (GTLS) from what we have today. The goal is to have a formal system, equivalent to that which exists in the physics community. Here we define how to perceive the role of time in biology. Section 8 describes the initial efforts to apply this general theory of living systems in many domains, with special emphasis on crossdisciplinary problems and multiple domains spanning both “hard” and “soft” sciences. The expected result is a coherent collection of integrated mathematical techniques. Section 9 discusses the first two test cases, project proposals, of our approach. They are designed to demonstrate the ability of our approach to address “wicked problems” which span across physics, chemistry, biology, societies and societal dynamics. The solutions require integrated measurable results at multiple levels known as “grand challenges” to existing methods. Finally, Section 10 adheres to an appeal for action, advocating the necessity for further long-term support of the INBIOSA program. -/- The report is concluded with preliminary non-exclusive list of challenging research themes to address, as well as required administrative actions. The efforts described in the ten sections of this White Paper will proceed concurrently. Collectively, they describe a program that can be managed and measured as it progresses. (shrink)

This paper compares the two known logical forms of hierarchy, both of which have been used in models of natural phenomena, including the biological. I contrast their general properties, internal formal relations, modes of growth (emergence) in applications to the natural world, criteria for applying them, the complexities that they embody, their dynamical relations in applied models, and their informational relations and semiotic aspects.

In this paper I provide a framework—what I refer to as ‘development theory’—for Ulanowicz’s ascendency theory of ecosystem development. Development theory is based in thermodynamics and information theory. A prominent feature of development theory is an understanding of senescence.

Levels of reality reflect one kind of complexity, which can be modeled using a specification hierarchy. Levels emerged during the Big Bang, as physical degrees of freedom became increasingly fixed as the expanding universe developed, and new degrees of freedom associated with higher levels opened up locally, requiring new descriptive semantics. History became embodied in higher level entities, which are increasingly individuated, aggregate patterns of lower level entities. Development is an epigenetic trajectory from vaguer to more definite and individuated embodiment, (...) punctuated by the emergence of new integrative levels. It is constrained by being subsumed by lower levels (e.g., physical dynamics) and may be guided by structural attractors as well as by internally stored information (e.g., genes) in the higher levels. I conjecture, on a thermodynamic basis, that the number of levels that become manifest in an expanding universe depends upon its rate of expansion. (shrink)

I distinguish Nature from the World. I also distinguish development from evolution. Development is progressive change and can be modeled as part of Nature, using a specification hierarchy. I have proposed a ‘canonical developmental trajectory’ of dissipative structures with the stages defined thermodynamically and informationally. I consider some thermodynamic aspects of the Big Bang, leading to a proposal for reviving final cause. This model imposes a ‘hylozooic’ kind of interpretation upon Nature, as all emergent features at higher levels would have (...) been vaguely and episodically present primitively in the lower integrative levels, and were stabilized materially with the developmental emergence of new levels. The specification hierarchy’s form is that of a tree, with its trunk in its lowest level, and so this hierarchy is appropriate for modeling an expanding system like the Universe. It is consistent with this model of differentiation during Big Bang development to view emerging branch tips as having been entrained by multiple finalities because of the top-down integration of the various levels of organization by the higher levels. (shrink)

A materialist construction of semiosis requires system embodiment at particular locales, in order to function as systems of interpretance. I propose that we can use a systemic model of scientific measurement to construct a systems view of semiosis. I further suggest that the categories required to understand that process can be used as templates when generalizing to biosemiosis and beyond. The viewpoint I advance here is that of natural philosophy—which, once granted, incurs no principled block to further generalization all the (...) way to pansemiotics—nearer to Peirce’s own very general perspective. This project requires a hylozooic framework, which I present in the form of a specification hierarchy, whereby physical dynamics subsume all other transactions at more highly developed integrative levels. The upshot of the paper is a proposal that meanings can be assimilated most generally to final causes. (shrink)

Recognition that biological systems are stabilized far from equilibrium by self-organizing, informed, autocatalytic cycles and structures that dissipate unusable energy and matter has led to recent attempts to reformulate evolutionary theory. We hold that such insights are consistent with the broad development of the Darwinian Tradition and with the concept of natural selection. Biological systems are selected that re not only more efficient than competitors but also enhance the integrity of the web of energetic relations in which they are embedded. (...) But the expansion of the informational phase space, upon which selection acts, is also guaranteed by the properties of open informational-energetic systems. This provides a directionality and irreversibility to evolutionary processes that are not reflected in current theory.For this thermodynamically-based program to progress, we believe that biological information should not be treated in isolation from energy flows, and that the ecological perspective must be given descriptive and explanatory primacy. Levels of the ecological hierarchy are relational parts of ecological systems in which there are stable, informed patterns of energy flow and entropic dissipation. Isomorphies between developmental patterns and ecological succession are revealing because they suggest that much of the encoded metabolic information in biological systems is internalized ecological information. The geneological hierarchy, to the extent that its information content reflects internalized ecological information, can therefore be redescribed as an ecological hierarchy. (shrink)

We are concerned with two modes of describing the dynamics of natural systems. Global descriptions require simultaneous global coordination of all dynamical operations. Global dynamics, including mechanics, remain invariant in the absence of external perturbation. But, failing impossible global coordination, dynamical operations could actually become coordinated only locally. In local records, as in global ones, the law of the excluded middle would be strictly observed, but without global coordination it could only be fullfilled sequentially by passing causative factors forward onto (...) subsequent contiguous operations.The local dynamics of sequential operations would be indefinite with regard to how commitments will be made which will avoid violating the law of the excluded middle, but any resulting record will be as definite as if there had been global coordination. While maintaining an agential capacity for making contingent choices internally, local dynamics could be cumulated into a global record of seemingly simultaneous operations. Natural selection within a framework of local dynamics would have a capacity for making opportunistic commitments, but its effects in a posterior record can be reduced to the mechanistic neodarwinian version as if there had been a global dynamics. However, the resulting global description falsifies the actual material nature of the dynamics. (shrink)

This paper presents a viewpoint on natural philosophy focusing on the organization of substance, as well as its changes as invited by the Second Law of thermodynamics. Modes of change are pointed to as definitive of levels of organization; these include physical, chemical, and biological modes of change. Conceptual uses of the subsumptive hierarchy format are employed throughout this paper. Developmental change in dissipative structures is examined in some detail, generating an argument for the use of final causality in studies (...) of natural systems. Considerations of ‘internalism’ in science are presented along the way. (shrink)

Appeals to science as a help in constructing policy on complex issues often assume that science has relatively clear-cut, univocal answers. That is not so today in the environmentally crucial fields of ecology and evolutionary biology. The social role of science has been as a source of information to be used in the prediction and domination of nature. Its perspectives are finely honed for such purposes. However, other more conscientious perspectives are now appearing within science, and we provide an example (...) here in rebuttal to the claim that there is no warrant from within ecology for ecosystem moral considerability. (shrink)

Foremost among the tasks facing a semiotically-informed modeling of natural open systems is the recognition and representation of self-organization. This forces attention on process, time, and energetics to complement the conventional semiotic bias toward structure, space, and informatics. While self -organization might be captured in numerous operational idioms, we suggest that the fundamentally distinctive formal structures of (a) development (intrinsic predictability) and (b) evolution (unexpected change through change in contextual meaning) constitute thewarp and woof of virtually all observations on systems (...) undergoing change, and that, since these represent complementary orientations toward phenomena generally, interaction of these styles of change within systems can lead to generic models of enormous utility in many fields. (shrink)

This article traces my attempts to come to grips with the problem of change. Systems science deals with general principles, but, as with science in general, is wedded to mechanistic models. Natural systems are not machines, are generative, and can change unpredictably. An example is given showing that explicit dynamical models are subverted by the present moment, which is non-existent in them. This moment can be modeled by a compositional hierarchy, but no change happens therein. Subsumptive hierarchies can serve as (...) metaperspectives on change, modeling stages of development. The Second Law of thermodynamics provides the motivation for development, which can be modeled generally using thermodynamic and information theoretic (infodynamic) concepts. Development is progressive change, constitutive of different systems, and goes from vagueness toward increasingly more definite embodiment, ending up in senescence, which derives from information overload. While becoming increasingly burdened with information, the present moment, as such, still evades this developmental systematicity. Internalist thinking has emerged as an attempt to further come to grips with it. (shrink)

Appeals to science as a help in constructing policy on complex issues often assume that science has relatively clear-cut, univocal answers. That is not so today in the environmentally crucial fields of ecology and evolutionary biology. The social role of science has been as a source of information to be used in the prediction and domination of nature. Its perspectives are finely honed for such purposes. However, other more conscientious perspectives are now appearing within science, and we provide an example (...) here in rebuttal to the claim that there is no warrant from within ecology for ecosystem moral considerability. (shrink)