Search Results (11)

Emergent properties are properties of a whole that cannot be reduced to the properties of its parts. Properties of a system can be defined as relations between a particular input given to a system and its corresponding output. From this perspective, whole systems formed by coupling component systems have properties different from the properties of their components. Wholes tend to arise spontaneously through a process of self-organization, in which components randomly interact until they settle in a stable configuration that in general cannot be predicted from the properties of the components. This configuration constrains the relations between the components, thus defining emergent “laws” that downwardly cause the further behavior of the components. Thus, emergent wholes and their properties arise in a simple and natural manner. Full article

Traditionally, scientists tend to approach cancer research in a reductionistic way: aiming at uncovering underlying, separate components in malignant processes. And indeed, great progress has been made by reducing the development of a tumor to single, specific genes and mutations. For instance, familial adenomatous polyposis (FAP) could be reduced to a germline mutation in the Adenomatous Polyposis Coli (APC) gene. The escape of tumor cells from immune surveillance could be reduced to the tumor expression of immune checkpoints, resulting in new approaches in tumor therapy by applying immune checkpoint inhibitors. However, a germline mutation in APC is not 1:1 related to colorectal cancer (CRC), and only some patients respond to immune checkpoint inhibitors. The point here is that biological systems, also comprising cancer, have properties that cannot be reduced to single components. The cooperation of the single components results in new, emergent properties. The outcome of an interaction in a complex network, like the immune system, depends on the many cell types involved and the numerous molecules that interact and activate or inhibit pathways. The way the composing elements are organized is a causal factor in itself for any emergent property. The rise of genomic analysis at the end of the previous century, enabling us to sequence a full genome at the DNA and RNA levels, has initiated an awareness of the need for ‘systems biology’: to consider a full system and how it is organized, in all of its aspects, to understand biological pathways and their outcomes. In this review, we outline the prospects and limitations of systems biology in cancer research and propose a causal framework that integrates upward and downward causation and multiple realizability to understand the emergent properties of tumors that determine the dynamics of tumor development. Full article

This paper discusses complexity theory, that is, the many theories that have been proposed for emergence of complexity from the underlying physics. Our aim is to identify which aspects have turned out to be the more fundamental ones as regards the emergence of biology, engineering, and digital computing, as opposed to those that are in fact more peripheral in these contexts. In the cases we consider, complexity arises via adaptive modular hierarchical structures that are open systems involving broken symmetries. Each emergent level is causally effective because of the meshing together of upwards and downwards causation that takes place consistently with the underlying physics. Various physical constraints limit the outcomes that can be achieved. The underlying issue concerns the origin of consciousness and agency given the basis of life in physics, which is structured starting from symmetries and variational principles with no trace of agency. A possible solution is to admit that consciousness is an irreducible emergent property of matter. Full article

This paper considers how a classification of causal effects as comprising efficient, formal, material, and final causation can provide a useful understanding of how emergence takes place in biology and technology, with formal, material, and final causation all including cases of downward causation; they each occur in both synchronic and diachronic forms. Taken together, they underlie why all emergent levels in the hierarchy of emergence have causal powers (which is Noble’s principle of biological relativity) and so why causal closure only occurs when the upwards and downwards interactions between all emergent levels are taken into account, contra to claims that some underlying physics level is by itself causality complete. A key feature is that stochasticity at the molecular level plays an important role in enabling agency to emerge, underlying the possibility of final causation occurring in these contexts. Full article

Systems biology is established as an integrative computational analysis methodology with practical and theoretical applications in clinical cardiology. The integration of genetic and molecular components of a disease produces interacting networks, modules and phenotypes with clinical applications in complex cardiovascular entities. With the holistic principle of systems biology, some of the features of complexity and natural progression of cardiac diseases are approached and explained. Two important interrelated holistic concepts of systems biology are described; the emerging field of personalized medicine and the constraint-based thinking with downward causation. Constraints in cardiovascular diseases embrace three scientific fields related to clinical cardiology: biological and medical constraints; constraints due to limitations of current technology; and constraints of general resources for better medical coverage. Systems healthcare and personalized medicine are connected to the related scientific fields of: ethics and legal status; data integration; taxonomic revisions; policy decisions; and organization of human genomic data. Full article

A fundamental problem regarding the storm–jet stream interaction in the extratropical atmosphere is how energy and information are exchanged between scales. While energy transfer has been extensively investigated, the latter has been mostly overlooked, mainly due to a lack of appropriate theory and methodology. Using a recently established rigorous formalism of information flow, this study attempts to examine the problem in the setting of a three-dimensional quasi-geostrophic zonal jet, with storms excited by a set of optimal perturbation modes. We choose for this study a period when the self-sustained oscillation is in quasi-equilibrium, and when the energetics mimick the mid-latitude atmospheric circulation where available potential energy is cascaded downward to smaller scales, and kinetic energy is inversely transferred upward toward larger scales. By inverting a three-dimensional elliptic differential operator, the model is first converted into a low-dimensional dynamical system, where the components correspond to different time scales. The information exchange between the scales is then computed through ensemble prediction. For this particular problem, the resulting cross-scale information flow is mostly from smaller scales to larger scales. That is to say, during this period, this model extratropical atmosphere is dominated by a bottom-up causation, as collective patterns emerge out of independent entities and macroscopic thermodynamic properties evolve from random molecular motions. This study makes a first step toward an important field in understanding the eddy–mean flow interaction in weather and climate phenomena such as atmospheric blocking, storm track, North Atlantic Oscillation, to name a few. Full article

Using insights from cybernetics and an information-based understanding of biological systems, a precise, scientifically inspired, definition of free-will is offered and the essential requirements for an agent to possess it in principle are set out. These are: (a) there must be a self to self-determine; (b) there must be a non-zero probability of more than one option being enacted; (c) there must be an internal means of choosing among options (which is not merely random, since randomness is not a choice). For (a) to be fulfilled, the agent of self-determination must be organisationally closed (a “Kantian whole”). For (c) to be fulfilled: (d) options must be generated from an internal model of the self which can calculate future states contingent on possible responses; (e) choosing among these options requires their evaluation using an internally generated goal defined on an objective function representing the overall “master function” of the agent and (f) for “deep free-will”, at least two nested levels of choice and goal (d–e) must be enacted by the agent. The agent must also be able to enact its choice in physical reality. The only systems known to meet all these criteria are living organisms, not just humans, but a wide range of organisms. The main impediment to free-will in present-day artificial robots, is their lack of being a Kantian whole. Consciousness does not seem to be a requirement and the minimum complexity for a free-will system may be quite low and include relatively simple life-forms that are at least able to learn. Full article

Metabolic disorders are a key problem in the transition period of dairy cows and often appear before the onset of further health problems. They mainly derive from difficulties the animals have in adapting to changes and disturbances occurring both outside and inside the organisms and due to varying gaps between nutrient supply and demand. Adaptation is a functional and target-oriented process involving the whole organism and thus cannot be narrowed down to single factors. Most problems which challenge the organisms can be solved in a number of different ways. To understand the mechanisms of adaptation, the interconnectedness of variables and the nutrient flow within a metabolic network need to be considered. Metabolic disorders indicate an overstressed ability to balance input, partitioning and output variables. Dairy cows will more easily succeed in adapting and in avoiding dysfunctional processes in the transition period when the gap between nutrient and energy demands and their supply is restricted. Dairy farms vary widely in relation to the living conditions of the animals. The complexity of nutritional and metabolic processes Animals 2015, 5 979 and their large variations on various scales contradict any attempts to predict the outcome of animals’ adaptation in a farm specific situation. Any attempts to reduce the prevalence of metabolic disorders and associated production diseases should rely on continuous and comprehensive monitoring with appropriate indicators on the farm level. Furthermore, low levels of disorders and diseases should be seen as a further significant goal which carries weight in addition to productivity goals. In the long run, low disease levels can only be expected when farmers realize that they can gain a competitive advantage over competitors with higher levels of disease. Full article

In this review I show that four major kinds of theoretical approaches have been used to explain the scaling of metabolic rate in cells, organisms and groups of organisms in relation to system size. They include models focusing on surface-area related fluxes of resources and wastes (including heat), internal resource transport, system composition, and various processes affecting resource demand, all of which have been discussed extensively for nearly a century or more. I argue that, although each of these theoretical approaches has been applied to multiple levels of biological organization, none of them alone can fully explain the rich diversity of metabolic scaling relationships, including scaling exponents (log-log slopes) that vary from ~0 to >1. Furthermore, I demonstrate how a synthetic theory of metabolic scaling can be constructed by including the context-dependent action of each of the above modal effects. This “contextual multimodal theory” (CMT) posits that various modulating factors (including metabolic level, surface permeability, body shape, modes of thermoregulation and resource-transport, and other internal and external influences) affect the mechanistic expression of each theoretical module. By involving the contingent operation of several mechanisms, the “meta-mechanistic” CMT differs from most metabolic scaling theories that are deterministically mechanistic. The CMT embraces a systems view of life, and as such recognizes the open, dynamic nature and complex hierarchical and interactive organization of biological systems, and the importance of multiple (upward, downward and reciprocal) causation, biological regulation of resource supply and demand and their interaction, and contingent internal (system) and external (environmental) influences on metabolic scaling, all of which are discussed. I hope that my heuristic attempt at building a unifying theory of metabolic scaling will not only stimulate further testing of all of the various subtheories composing it, but also foster an appreciation that many current models are, at least in part, complementary or even synergistic, rather than antagonistic. Further exploration about how the scaling of the rates of metabolism and other biological processes are interrelated should also provide the groundwork for formulating a general metabolic theory of biology. Full article

We thank Dr. Baverstock [1] for his interest in reading our article and his time in writing his comments for our work [2]. We, however, respectfully disagree with his statement that we made “two category errors” associated with the assessment of the occurrence of “genomic instability” by determining the frequencies of delayed- or late-occurring chromosomal damage. Our disagreement is based upon the well-known fact that radiation-induced genomic instability (or delayed/late-occurring damage) can be manifested in many ways. These include late-occurring chromosomal damage, or mutations, or gene expression, or gene amplifications, or transformation, or microsatellite instability, or cell killing [3–9]. Such phenomena have been detected many cell generations after irradiation. We agree that genomic instability may well be the consequence of epigenetic changes. Another mechanism mentioned by Dr. Bavertock as being probably unlikely is the reversibility of damage. This potential may not be discarded off-hand, as Dr. Baverstock prefers to do. There is much reproducible evidence of adaptive protection that depending on absorbed dose precisely may reverse early damage, and damage appearing late may be due to some form of residual damage letting the cell become genetically unstable. In other words, the argument by Dr. Baverstock regarding upward or downward causation appears to be rather speculative and far from being settled. Full article

Within recent discussions in the Philosophy of Mind, the nature of conscious phenomenal states or qualia (also called ‘raw feels’ or the feel of ‘what it is like to be’) has been an important focus of interest. Proponents of Mind-Body Type-Identity theories have claimed that mental states can be reduced to neurophysiological states of the brain. Others have denied that such a reduction is possible; for them, there remains an explanatory gap. In this paper, functionalist, physicalist, epiphenomenalist, and biological models of the mind are discussed and compared. Donald Davidson’s Anomalous Monism is proposed as a unifying framework for a non-reductive theory of qualia and consciousness. Downward Causation, Emergence through Symmetry-breaking, and Dynamical Systems Theory are used to show how consciousness and qualia emerge from their neural substrate and can also be causally efficacious. Full article