Integral Biomathics Reloaded: 2015

An updated survey of the research scope in Integral Biomathics

Stepping Beyond the Newtonian Paradigm in Biology. Towards an Integrable Model of Life: Accelerating Discovery in the Biological Foundations of Science

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

Evolutionary Analysis of Inter-Farm Transmission Dynamics in a Highly Pathogenic Avian Influenza Epidemic

Phylogenetic studies have largely contributed to better understand the emergence, spread and evolution of highly pathogenic avian influenza during epidemics, but sampling of genetic data has never been detailed enough to allow mapping of the spatiotemporal spread of avian influenza viruses during a single epidemic. Here, we present genetic data of H7N7 viruses produced from 72% of the poultry farms infected during the 2003 epidemic in the Netherlands. We use phylogenetic analyses to unravel the pathways of virus transmission between farms and between infected areas. In addition, we investigated the evolutionary processes shaping viral genetic diversity, and assess how they could have affected our phylogenetic analyses. Our results show that the H7N7 virus was characterized by a high level of genetic diversity driven mainly by a high neutral substitution rate, purifying selection and limited positive selection. We also identified potential reassortment in the three genes that we have tested, but they had only a limited effect on the resolution of the inter-farm transmission network. Clonal sequencing analyses performed on six farm samples showed that at least one farm sample presented very complex virus diversity and was probably at the origin of chronological anomalies in the transmission network. However, most virus sequences could be grouped within clearly defined and chronologically sound clusters of infection and some likely transmission events between farms located 0.8–13 Km apart were identified. In addition, three farms were found as most likely source of virus introduction in distantly located new areas. These long distance transmission events were likely facilitated by human-mediated transport, underlining the need for strict enforcement of biosafety measures during outbreaks. This study shows that in-depth genetic analysis of virus outbreaks at multiple scales can provide critical information on virus transmission dynamics and can be used to increase our capacity to efficiently control epidemics

Rights, Responsibilities and Resilience; or 'Auntie Phyllis and the Bloody Great Fork'

The evolution of human societies has been punctuated by a progressive multiplicity of declarations of the rights which more or less rigidly defined groups of humans, citizens or organisms could claim. The very idea of equilibrium in any dynamic environment depends on a balance between counteracting influences. The United Nations General Assembly’s Universal Declaration of Human Rights in 1948 was itself an important step forward, but where is the Universal Declaration of Human Responsibilities?[1] This question of equilibrium is fundamental to any concept of resilience, which although lacking a clear definition for human society as a whole does imply a sense of continuity or temporal sustainability. Sadly, although Spiritually-based movements have long focused on the advisability of pro/contra relational equilibria, Science has traditionally taken a view that the experimenter controls his or her subject, and that the relationship must of pragmatic and philosophic necessity be unidirectional. This imbalance did begin to break down during the twentieth century, with the introduction of quantum theory, but only within limited areas of investigation. Arguably, a turning point in the drift of global human attention towards recognition of the importance of environmental equilibrium was Rachel Carson’s publication in 1962 of Silent Spring, but it is only comparatively recently that fear of global warming has really begun to exercise our intellect. Fascinatingly, if unsurprisingly, most discussion of this possibly imminent phenomenon focuses on ‘who is to blame’, rather than whether the alleged causes should be addressed independently of whether catastrophe will follow or not. Science has journeyed onward in an unstated assumption that analysis and synthesis are symmetrical[2]. The long-held belief that it will ultimately be possible to establish a Theory of Everything from examination of the properties of elementary particles bears witness to this supposition; the macroscopic complexity of Nature indicates that such a belief is farcical. Although the more exact sciences have begun to move out of their ‘comfort zone’ of near-equilibrium quasi-linearity by tackling chaos and less-than-deterministic systems, they have yet to meet up with biology coming in the other direction. Inorganic nature can be addressed reasonably successfully by either digital or analog techniques, but life establishes multi-scalar systems based on compromise between the two and on variable relationships between local scalar and global non-scalar characters. Until now this has had very little impact on Science in general, particularly in the present socio-commercial climate where analog is bad and digital is good. The central issue for any overarching view of Nature, society and of their interaction is one of scale. How does, or should, an individual or group relate to local society in general or to planetary resilience? How do, or should, rights and responsibilities be integrated into a scheme which accepts the complexity of multi-scalar organisms and multi-scalar societies on a multi-scalar planet? This is, or should be, the central theme of any approach to resilience. But should it be a question which only concerns governance as a top-down ‘leave it to the politicians’ approach? Contextually identified concepts of top-down and bottom-up design or control abound in our surroundings, but neither of them can ever be efficiently viable on its own, nor can the two be simplistically integrated into a mono-rational system for which analysis and synthesis are asymmetrical. Careful examination of naturally-generated ‘hierarchical’ systems[3] leads to a recognition that purely scale-local organization can never be sufficient to guarantee any form of resilience in the face of either external or internal perturbation, never mind guaranteeing a resilience which can sustain ‘health and happiness’ for a system’s constituent elements. Inter-scalar transit in a multi-scalar system depends on global properties, which themselves depend on local phenomena, whether for an individual or a society. So, it seems that in addressing the resilience of our mono-rational multi-scalar societies, of multi-scalar organisms, on a multi-scalar planet, it would be reasonable to first think carefully about how multi-scalar natural systems operate. Will this be sufficient? No, although it will probably help somewhat. But maybe an important first step would be to address, in our own lives, and therefore at a very small scale, the balance between rights and responsibilities which will be necessary to support effectiveness of any future governance that, for all our sakes, targets resilient dynamic socio-planetary equilibrium. From small acorns do tall oak trees grow. [1] The establishment of such a document has indeed been addressed, most recently by the InterAction Council of Former Heads of State and Government, but it remains, unfortunately, without any overt consequences.   [2] For an extensive consideration of this relationship in the context of living organisms see Robert Rosen’s 1991 book Life Itself: A Comprehensive Inquiry into the Nature, Origin, and Fabrication of Life. [3] The reader should note that by ‘hierarchical’ we are looking towards systems which are neither uniquely top-down nor bottom-up in their organizational style

SYSTEM DUALITY: BIRATIONAL HIERARCHY

System theory, and most particularly hierarchy theory, must be consistent with philosophy. In his book “Logic in Reality”, Brenner reinforces the traditional philosophic position that an entity can only exist in relation to its non-existence. This leads to a duality in system theory which is consistent with the selective division of Nature into entity and ecosystem, where the two depend on different criteria and even different logics. A fascinating aspect of such a birational approach is that representations and properties only exist as intermediates between pairs of ideal extremes. Quantum logic, for example, no longer replaces post-Newtonian classical logic; it complements it, identifying all real entities as compromises between the two. This albeit philosophically non-traditional included middle is identical to that of the philosophical logic of Stéphane Lupasco, and to the implications of Brenner’s “Logic in Reality”. This presages a major philosophical change in the way Science can be carried out. What we wish to do is to bring all of Science under a generalized umbrella of entity and ecosystem, and then characterize different types of entity by their more or less important relationships with their relevant ecosystems. The most general way to do this is to move the ecosystemic paradigm up to the level of its encompassing logic, creating a complementary pair of conceivably different logics – one for the entity we are focusing on; one for the ecosystem within which it exists – and providing for their quasi-autonomous birational interaction. We present a representation of natural hierarchy which is itself dual in character, and counsel that monorational constructions are ineffective. As an example, we present a dual formulation of entropy. We conclude with an application of the model to large Organizations

GETTING (EMPIRICALLY) BACK TO(WARDS) (PRE-)(EXISTENTIAL) BASICS

Hierarchical systems are understandably of great interest because of the apparent difficulty in understanding them. They are, by their very nature, the result of some kind of evolution, whether of themselves or of some precursor or template. In many ways their developments parallel the evolution of organisms, in their environmental sensitivity and their existential dependence on some kind of relative cost function. Natural evolution is notorious for scavenging earlier evolved characteristics in its search for survivalist advantage, and consequently a current hierarchical instantiation may be far from its evolutionary template, and may consequently be inadvertently driven to extinction. A major source of this estrangement derives from a primary support for the establishment of hierarchy: the belief that formal fractionation of a large group of elements can lead to stronger cohesion and a more unified purpose. But where does this apparent contradiction come from? How is it that we can believe that the best way to unify a system is by splitting it up? In this paper we address the appearance of this phenomenon in the natural world, and relate its implementation to examples from many domains of systemic study

Living in Hyperscale: Internalization as a Search for Reunification

Living organisms survive through their generation and use of internal models of themselves and of their environments. Homo sapiens internalizes the environment through modeling in such a way that it can effectively be artificially present at any number of different external locations. While this capacity is clearly advantageous for survival, it may well have yet another 'meaning'. We believe that entities internalize their environment in a local attempt to reunify the fragmented global landscape of which they are a part. This paper charts the argumentational route which must be taken to justify this hypothesis