PDF version This talk explores three concepts of system in engineering: systems theory, systems approach, and systems engineering. They are exemplified in three dimensions of engineering: science, design, and management. Unifying the three system concepts is the idea of function: functional abstraction in theory, functional analysis in design, and functional requirements in management. Signifying what a system is for, function is a purposive notion absent in physical science, which aims to understand nature. It is prominent in engineering, which aims to (...) transform nature for serving the wants and needs of people. (shrink)
Several key areas in modeling the cardiovascular and respiratory control systems are reviewed and examples are given which reflect the research state of the art in these areas. Attention is given to the interrelated issues of data collection, experimental design, and model application including model development and analysis. Examples are given of current clinical problems which can be examined via modeling, and important issues related to model adaptation to the clinical setting.
Complex Systems Biology approaches are here considered from the viewpoint of Robert Rosen’s (M,R)-systems, Relational Biology and Quantum theory, as well as from the standpoint of computer modeling. Realizability and Entailment of (M,R)-systems are two key aspects that relate the abstract, mathematical world of organizational structure introduced by Rosen to the various physicochemical structures of complex biological systems. Their importance for understanding biological function and life itself, as well as for designing new strategies for treating diseases such as cancers, is (...) pointed out. The roles played by multiple metastable states in the “continuous uphill flow of Life” supported through internal bioenergetic processes that are coupled to essential inflows are also discussed in relation to dynamic realizations of (M,R)-systems. Furthermore, the roles played by the underlying, many-valued, quantum logics and symbolic computations for ultra-complex biological systems are also briefly discussed. (shrink)
Possible effects of interaction (cross-talk) between signaling pathways is studied in a system of Reaction–Diffusion (RD) equations. Furthermore, the relevance of spontaneous neurite symmetry breaking and Turing instability has been examined through numerical simulations. The interaction between Retinoic Acid (RA) and Notch signaling pathways is considered as a perturbation to RD system of axon-forming potential for N2a neuroblastoma cells. The present work suggests that large increases to the level of RA–Notch interaction can possibly have substantial impacts on neurite outgrowth and (...) on the process of axon formation. This can be observed by the numerical study of the homogeneous system showing that in the absence of RA–Notch interaction the unperturbed homogeneous system may exhibit different saddle-node bifurcations that are robust under small perturbations by low levels of RA–Notch interactions, while large increases in the level of RA–Notch interaction result in a number of transitions of saddle-node bifurcations into Hopf bifurcations. It is speculated that near a Hopf bifurcation, the regulations between the positive and negative feedbacks change in such a way that spontaneous symmetry breaking takes place only when transport of activated Notch protein takes place at a faster rate. (shrink)
Recently improved understanding of evolutionary processes suggests that tree-based phylogenetic analyses of evolutionary change cannot adequately explain the divergent evolutionary histories of a great many genes and gene complexes. In particular, genetic diversity in the genomes of prokaryotes, phages, and plasmids cannot be fit into classic tree-like models of evolution. These findings entail the need for fundamental reform of our understanding of molecular evolution and the need to devise alternative apparatus for integrated analysis of these genomes. We advocate the development (...) of integrative phylogenomics for analyzing these genomes and their histories, with tools suited to analyzing the importance of lateral gene transfer (LGT) and of DNA evolution in extra-cellular mobile genetic elements (e.g., viruses, plasmids). These phenomena greatly increase the complexity of relationships among interacting genetic partners, as they exchange functional genetic units. We examine the ontology of functional genetic units, interacting genetic partners, and emergent genetic associations, argue that these three categories of entities are required for a successful integrated phylogenomics. We conclude with arguments to suggest that the proposed new perspective and associated tools are suitable, and perhaps required, as a replacement for the bifurcating trees that have dominated evolutionary thinking for the last 150 years. (shrink)
Standard microbial evolutionary ontology is organized according to a nested hierarchy of entities at various levels of biological organization. It typically detects and defines these entities in relation to the most stable aspects of evolutionary processes, by identifying lineages evolving by a process of vertical inheritance from an ancestral entity. However, recent advances in microbiology indicate that such an ontology has important limitations. The various dynamics detected within microbiological systems reveal that a focus on the most stable entities (or features (...) of entities) over time inevitably underestimates the extent and nature of microbial diversity. These dynamics are not the outcome of the process of vertical descent alone. Other processes, often involving causal interactions between entities from distinct levels of biological organisation, or operating at different time scales, are responsible not only for the destabilisation of pre-existing entities, but also for the emergence and stabilisation of novel entities in the microbial world. In this article we consider microbial entities as more or less stabilised functional wholes, and sketch a network-based ontology that can represent a diverse set of processes including, for example, as well as phylogenetic relations, interactions that stabilise or destabilise the interacting entities, spatial relations, ecological connections, and genetic exchanges. We use this pluralistic framework for evaluating (i) the existing ontological assumptions in evolution (e.g. whether currently recognized entities are adequate for understanding the causes of change and stabilisation in the microbial world), and (ii) for identifying hidden ontological kinds, essentially invisible from within a more limited perspective. We propose to recognize additional classes of entities that provide new insights into the structure of the microbial world, namely “processually equivalent” entities, “processually versatile” entities, and “stabilized” entities. (shrink)
The levels that compose biological hierarchies each have their own energetic, spatial and temporal structure. Indeed, it is the discontinuity in energy relationships between levels, as well as the similarity of sub-systems that support them, that permits levels to be defined. In this paper, the temporal structure of living hierarchies, in particular that pertaining to Human society, is examined. Consideration is given to the period defining the lifespan of entities at each level and to a periodic event considered fundamental to (...) the maintenance of that level. The ratio between the duration of these two periods is found to be approximately 2.5 × 104. A similar relationship is found when lower, non-living levels of molecules and atoms are considered. This suggests that there is a constant factor of amplification between analogous periodic events at successive levels of the Human hierarchy. (shrink)
Using the Burgess Shale controversies as a case-study, this paper argues that controversies within different domains may interact as to create a situation of "complicated intricacies," where the practicing scientist has to navigate through a context of multiple thought collectives. To some extent each of these collectives has its own dynamic complete with fairly negotiated standards for investigation and explanation, theoretical background assumptions and certain peculiarities of practice. But the intellectual development in one of these collectives may "spill over" having (...) far reaching consequences for the treatment of apparently independent epistemic problems that are subject of investigation in other thought collectives. For the practicing scientist it is necessary to take this complex web of interactions into account in order to be able to navigate in such a situation. So far most studies of academic science have had a tendency to treat the practicing scientist as members of a single (enclosed) thought collective that stands intellectually isolated from other similar entities unless the discipline was in a state of crisis of paradigmatic proportions. The richness and complexity of Burgess Shale debate shows that this encapsulated kind of analysis is not enough. (shrink)
This thematic issue addresses questions of constraints on the evolution of form—physical, biological, and technical. Here, form is defined as an embodiment of a specific structure, which can be hierarchically different yet emerge from the same processes. The focus of this contribution is about how developmental biology and paleontology can be better integrated and compared in order to produce hypotheses about the evolution of form. The constraints on current EvoDevo research stem from the disconnect in the focus of study for (...) developmental geneticists and evolutionary morphologists; the former being interested in early developmental events at a molecular level in a model animal, the latter in late developmental events or comparison between adult forms, at a structural level in non-model animals. In order to truly integrate information from both fields in our understanding of evolutionary processes, morphology needs to be reintegrated in the study of gene expression, and its time frame needs to be extended beyond early developmental stages. Gene expression in non-model organisms also needs to be studied in order to gain perspective into primitive patterning at evolutionary nodes. Hypotheses formed by the comparison of expression patterns and morphologies seen in extant species can then be tested against forms found in the fossil record, coming closer to understanding the mechanisms underlying evolution. (shrink)
The paper discusses how systems biology is working toward complex accounts that integrate explanation in terms of mechanisms and explanation by mathematical models—which some philosophers have viewed as rival models of explanation. Systems biology is an integrative approach, and it strongly relies on mathematical modeling. Philosophical accounts of mechanisms capture integrative in the sense of multilevel and multifield explanations, yet accounts of mechanistic explanation (as the analysis of a whole in terms of its structural parts and their qualitative interactions) have (...) failed to address how a mathematical model could contribute to such explanations. I discuss how mathematical equations can be explanatorily relevant. Several cases from systems biology are discussed to illustrate the interplay between mechanistic research and mathematical modeling, and I point to questions about qualitative phenomena (rather than the explanation of quantitative details), where quantitative models are still indispensable to the explanation. Systems biology shows that a broader philosophical conception of mechanisms is needed, which takes into account functional-dynamical aspects, interaction in complex networks with feedback loops, system-wide functional properties such as distributed functionality and robustness, and a mechanism’s ability to respond to perturbations (beyond its actual operation). I offer general conclusions for philosophical accounts of explanation. (shrink)
The biological sciences study (bio)complex living systems. Research directed at the mechanistic explanation of the "live" state truly requires a pluralist research program, i.e. BioComplexity research. The program should apply multiple intra-level and inter-level theories and methodologies. We substantiate this thesis with analysis of BioComplexity: metabolic and modular control analysis of metabolic pathways, emergence of oscillations, and the analysis of the functioning of glycolysis.
The present thesis, compatible with Darwinian theory, endeavours to provide original answers to the question of why the evolution of species leads to beings more complex than those existing before. It is based on the repetition of two main principles alleged to play a role in evolution towards complexity, i.e. "juxtaposition" and "integration". Juxtaposition is the addition of identical entities. Integration is the modification, or specialisation, of these entities, leading to entities on a higher level, which use the previous entities (...) as units. Several concrete examples of the process are given, at the genetic level (introns), at the anatomical level and at the social level. Structures where integration at one level leaves the units at a lower level in a state of relative autonomy can be describedusing the metaphor of the "mosaic", and the description can also be applied to the human brain and functioning of thought, where essential functions such as language or memory have a mosaic structure. (shrink)
Scientists have attempted several times to define the notion of complexity. A proper definition uses elements of three sets: a set of sites, as set of connections, and a set of nodes coincides with the set. Sites and connections can be translated into terms of graph theory as vertices and edges, which enables to consider complexity as an associated graph.Thus complexity of a system (or a structure) will be defined as the number of possible figures and aspects which are obtained (...) by combining vertices and edges. Complexity is the product of two factors, the first factor is tied to the combination of nodes called mutability and the second is tied to the combination of edges called liability. (shrink)
There are two different ways of defining complexity.1) Traditionally, the word "complexity" is considered synonymous to "organization". The transformation of species is an expression of victory against random indifferencism.
Catastrophe Theory was developed in an attempt to provide a form of Mathematics particularly apt for applications in the biological sciences. It was claimed that while it could be applied in the more conventional physical way, it could also be applied in a new metaphysical way, derived from the Structuralism of Saussure in Linguistics and Lévi-Strauss in Anthropology.Since those early beginnings there have been many attempts to apply Catastrophe Theory to Biology, but these hopes cannot be said to have been (...) fully realised. (shrink)
Darwin's greatest accomplishment was to show how life might be explained as the result of natural selection. But does Darwin's theory mean that life was unintended? William A. Dembski argues that it does not. In this book Dembski extends his theory of intelligent design. Building on his earlier work in The Design Inference (Cambridge, 1998), he defends that life must be the product of intelligent design. Critics of Dembski's work have argued that evolutionary algorithms show that life can be explained (...) apart from intelligence. But by employing powerful recent results from the No Free Lunch Theory, Dembski addresses and decisively refutes such claims. As the leading proponent of intelligent design, Dembski reveals a designer capable of originating the complexity and specificity found throughout the cosmos. Scientists and theologians alike will find this book of interest as it brings the question of creation firmly into the realm of scientific debate. (shrink)
A short review of complexity research from the perspective of history and philosophy of biology is presented. Complexity and its emergence has scientific and metaphysical meanings. From its beginning, biology was a science of complex systems, but with the advent of electronic computing and the possibility of simulating mathematical models of complicated systems, new intuitions of complexity emerged, together with attempts to devise quantitative measures of complexity. But can we quantify the complex?
Instead of commenting directly on Foundations of Language: Brain, Meaning, Grammar, Evolution, I provide some remarks from an interdisciplinary view. Language theory is examined from the perspective of the theory of complex systems. The gestural-vocal dichotomy, network theory, evolutionary mechanisms/algorithms, chaos theory, and constructive approach are briefly mentioned.
Richard Dawkins has popularized an argument that he thinks sound for showing that there is almost certainly no God. It rests on the assumptions (1) that complex and statistically improbable things are more difficult to explain than those that are not and (2) that an explanatory mechanism must show how this complexity can be built up from simpler means. But what justifies claims about the designer’s own complexity? One comes to a different understanding of order and of simplicity when one (...) considers the psychological counterpart of information. In assessing his treatment of biological organisms as either self-programmed machines or algorithms, I show how self-generated organized complexity does not fit well with our knowledge of abduction and of information theory as applied to genetics. I also review some philosophical proposals for explaining how the complexity of the world could be externally controlled if one wanted to uphold a traditional understanding of divine simplicity. (shrink)
My understanding is that proximate explanations concern adaptive mechanism and that ultimate explanations concern adaptive rationale. Viewed in this light, the two kinds of explanation are quite distinct, but they interact in a complementary way to give a full understanding of biological adaptations. In contrast, Laland et al. (2013)—following a literal reading of Mayr (Science 134:1501–1506, 1961)—have characterized ultimate explanations as concerning any and all mechanisms that have operated over the course of an organism’s evolutionary history. This has unfortunate consequences, (...) such as allowing random drift to form the basis for ultimate explanations, and allowing proximate and ultimate explanations to bleed into each other until their distinction is meaningless. Here, I suggest Laland et al’s explanatory framework of “reciprocal causation” is not conducive to successful biological science, and that they have misunderstood key elements of the theory of Darwinian adaptation. (shrink)
Darwin's theory of natural selection is as applicable to the analysis of the behavior of organisms as it is to their origins. Skinner's theoretical writings have guided operant psychologists in this area. The behavioral account of selection by Donahoe and Palmer (1994) is positively compared to the points on operant selection made by Hull et al. The “general account of selection” was found to be useful.
The established definition of replication in terms of the conditions of causality, similarity and information transfer is very broad. We draw inspiration from the literature on self-reproducing automata to strengthen the notion of information transfer in replication processes. To the triple conditions of causality, similarity and information transfer, we add a fourth condition that defines a “generative replicator” as a conditional generative mechanism, which can turn input signals from an environment into developmental (...) instructions. Generative replication must have the potential to enhance complexity, which in turn requires that developmental instructions are part of the information that is transmitted in replication. Demonstrating the usefulness of the generative replicator concept in the social domain, we identify social generative replicators that satisfy all of the four proposed conditions. (shrink)
While some branches of complexity theory are advancing rapidly, the same cannot be said for our understanding of emergence. Despite a complete knowledge of the rules underlying the interactions between the parts of many systems, we are often baffled by their sudden transitions from simple to complex. Here I propose a solution to this conceptual problem. Given that emergence is often the result of many interactions occurring simultaneously in time and space, an ability to intuitively grasp it would require the (...) ability to consciously think in parallel. A simple exercise is used to demonstrate that we do not possess this ability. Our surprise at the behaviour of cellular automata models, and the natural cases of pattern formation they mimic, is then explained from this perspective. This work suggests that the cognitive limitations of the mind can be as significant a barrier to scientific progress as the limitations of our senses. (shrink)
This article discusses my book, Origins of Order: Self Organization and Selection in Evolution, in the context of the emerging sciences of complexity. Origins, due out of Oxford University Press in early 1992, attempts to lay out a broadened theory of evolution based on the marriage of unexpected and powerful properties of self organization which arises in complex systems, properties which may underlie the origin of life itself and the emergence of order in ontogeny, and the continuing action of natural (...) selection. The three major themes are: 1) that such self organized properties lie to hand for selection's further molding; 2) hence that the order we see is not due to selection alone, but in part reflects the order selection has always acted upon; 3) and finally that the marriage of natural order and natural selection may inevitably lead living entitites to a novel organized state, lying on the edge between order and chaos, as the inevitable evolutionary attractor of selection for the capacity to adapt. (shrink)
Ultimately we will only understand biological agency when we have developed a theory of the organization of biological processes, and science is still a long way from attaining that goal. It may be possible nonetheless to develop a list of necessary conditions for the emergence of minimal biological agency. The authors offer a model of molecular autonomous agents which meets the five minimal physical conditions that are necessary (and, we believe, conjointly sufficient) for applying agential language in biology: autocatalytic reproduction; (...) work cycles; boundaries for reproducing individuals; self-propagating work and constraint construction; and choice and action that have evolved to respond to food or poison. When combined with the arguments from preadaptation and multiple realizability, the existence of these agents is sufficient to establish ontological emergence as against what one might call Weinbergian reductionism. Minimal biological agents are emphatically not conscious agents, and accepting their existence does not commit one to any robust theory of human agency. Nor is there anything mystical, dualistic, or non-empirical about the emergence of agency in the biosphere. Hence the emergence of molecular autonomous agents, and indeed ontological emergence in general, is not a negation of or limitation on careful biological study but simply one of its implications. (shrink)
Our aim in this article is to attempt to discuss propagating organization of process, a poorly articulated union of matter, energy, work, constraints and that vexed concept, “information”, which unite in far from equilibrium living physical systems. Our hope is to stimulate discussions by philosophers of biology and biologists to further clarify the concepts we discuss here. We place our discussion in the broad context of a “general biology”, properties that might well be found in life anywhere in the cosmos, (...) freed from the specific examples of terrestrial life after 3.8 billion years of evolution. By placing the discussion in this wider, if still hypothetical, context, we also try to place in context some of the extant discussion of information as intimately related to DNA, RNA and protein transcription and translation processes. While characteristic of current terrestrial life, there are no compelling grounds to suppose the same mechanisms would be involved in any life form able to evolve by heritable variation and natural selection. In turn, this allows us to discuss at least briefly, the focus of much of the philosophy of biology on population genetics, which, of course, assumes DNA, RNA, proteins, and other features of terrestrial life. Presumably, evolution by natural selection—and perhaps self-organization—could occur on many worlds via different causal mechanisms. Here we seek a non-reductionist explanation for the synthesis, accumulation, and propagation of information, work, and constraint, which we hope will provide some insight into both the biotic and abiotic universe, in terms of both molecular self reproduction and the basic work energy cycle where work is the constrained release of energy into a few degrees of freedom. The typical requirement for work itself is to construct those very constraints on the release of energy that then constitute further work. Information creation, we argue, arises in two ways: first information as natural selection assembling the very constraints on the release of energy that then constitutes work and the propagation of organization. Second, information in a more extended sense is “semiotic”, that is about the world or internal state of the organism and requires appropriate response. The idea is to combine ideas from biology, physics, and computer science, to formulate explanatory hypotheses on how information can be captured and rendered in the expected physical manifestation, which can then participate in the propagation of the organization of process in the expected biological work cycles to create the diversity in our observable biosphere. Our conclusions, to date, of this enquiry suggest a foundation which views information as the construction of constraints, which, in their physical manifestation, partially underlie the processes of evolution to dynamically determine the fitness of organisms within the context of a biotic universe. (shrink)
This article presents results from simulations studying the hypothesis that mechanisms for landmark-based navigation could have served as preadaptations for compositional language. It is argued that sharing directions would significantly have helped bridge the gap between general and language-specific cognitive faculties. A number of different levels of navigational and communicative abilities are considered, resulting in a range of possible evolutionary paths. The selective pressures for, resp. against, increased complexity in either faculty are then evaluated for a range of environments. The (...) study aims specifically to identify whether there is a viable evolutionary path leading to compositional language, and if so, under what circumstances. The results show that environmental conditions can render a step towards more complex communication either desirable or harmul, and suggest that very specific initial conditions and changes in the environment, resp. the ecological niche occupied, would have been needed to select for compositional language. Subject to these conditions, a (proto)language using order, but no hierarchical structure could evolve. This represents a middle ground, which brings closer hypotheses about syntax that have so far appeared difficult to reconcile. (shrink)
Biological objects are often constructive dynamic systems whose structures evolve as a consequence of their internal dynamics, which in turn is affected by the overall structure. As very few tools are presently adapted to tackle constructive dynamic systems, they constitute fascinating challenges for modeling/simulation. In cell biology, the secretory process in eukaryotic cells corresponds to this type of system, as it appears to autonomously generate new structures as a result of its molecular dynamics. Here I briefly review the only documented (...) case of a membrane-bounded intracellular compartment whose very existence strictly depends on its continued functioning. Indeed, the Golgi apparatus of the yeast Saccharomyces cerevisiae appears at steady-state as a continuously renewed set of transitory membrane-bounded structures that self-mature, rather than as a permanent entity. On the basis of this case and of recent advances in related molecular studies, a detailed model is proposed, that encompasses the birth of a yeast Golgi element and bridges its molecular and morphogenetic aspects. This model is extended to briefly outline three evolutionary inventions, from S. cerevisiae to another yeast, Pichia pastoris, on to plant, and on to animal cells: stacking, stabilizing and aggregating the primary Golgi elements. (shrink)