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1.
Louie AH 《化学与生物多样性》2007,4(10):2296-2314
This essay contains a few of my interpretations of Robert Rosen's conception of Nature. I shall study the four notions that form the core of his whole-lifetime's scientific work: simple system, mechanism, complex system, and organism. Their set-theoretic interconnections culminate in Rosen's new taxonomy of natural systems. 相似文献
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Thomas SR 《化学与生物多样性》2007,4(10):2407-2414
The widespread use of the term Systems Biology (SB) signals a welcome recognition that organisms must be understood as integrated systems. Although just what this is taken to mean varies from one group to another, it generally implies a focus on biological functions and processes rather than on biological parts and a reliance on mathematical modeling to arrive at an understanding of these biological processes based on biological observations or measurements. SB, thus, falls directly in the line of reflection carried out by Robert Rosen throughout his work. In the present article, we briefly introduce the various currents of SB and then point out several ways Rosen's work can be used to avoid certain pitfalls associated with the use of dynamical systems models for the study of complex systems, as well as to inspire a productive path forward based on loosely organized cooperation among dispersed laboratories. 相似文献
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Mikulecky DC 《化学与生物多样性》2007,4(10):2480-2491
Two distinctly different worldviews dominate today's thinking in science and in the world of ideas outside of science. Using the approach advocated by Robert M. Hutchins, it is possible to see a pattern of interaction between ideas in science and in other spheres such as philosophy, religion, and politics. Instead of compartmentalizing these intellectual activities, it is worthwhile to look for common threads of mutual influence. Robert Rosen has created an approach to scientific epistemology that might seem radical to some. However, it has characteristics that resemble ideas in other fields, in particular in the writings of George Lakoff, Leo Strauss, and George Soros. Historically, the atmosphere at the University of Chicago during Hutchins' presidency gave rise to Rashevsky's relational biology, which Rosen carried forward. Strauss was writing his political philosophy there at the same time. One idea is paramount in all this, and it is Lakoff who gives us the most insight into how the worldviews differ using this idea. The central difference has to do with causality, the fundamental concept that we use to build a worldview. Causal entailment has two distinct forms in Lakoff 's analysis: direct causality and complex causality. Rosen's writings on complexity create a picture of complex causality that is extremely useful in its detail, grounding in the ideas of Aristotle. Strauss asks for a return to the ancients to put philosophy back on track. Lakoff sees the weaknesses in Western philosophy in a similar way, and Rosen provides tools for dealing with the problem. This introduction to the relationships between the thinking of these authors is meant to stimulate further discourse on the role of complex causal entailment in all areas of thought, and how it brings them together in a holistic worldview. The worldview built on complex causality is clearly distinct from that built around simple, direct causality. One important difference is that the impoverished causal entailment that accompanies the machine metaphor in science is unable to give us a clear way to distinguish living organisms from machines. Complex causality finds a dichotomy between organisms, which are closed to efficient cause, and machines, which require entailment from outside. An argument can be made that confusing living organisms with machines, as is done in the worldview using direct cause, makes religion a necessity to supply the missing causal entailment. 相似文献
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Prideaux JA 《化学与生物多样性》2007,4(10):2415-2426
In the work 'Life Itself', Rosen showed that a formal mechanism cannot be 'closed to efficient cause'. Additionally, he claimed that organisms are 'closed to efficient cause' and that, by logical extension, organisms cannot be mechanisms. This paper shows that it is possible for mechanisms to be 'nearly closed to efficient cause', with the requirement that some unentailed efficient-cause agents are placed inside the system. Populations of these 'nearly closed to efficient cause' systems can be defined based on the ability to isolate each component in its own 'reaction chamber'. Diagrams from these populations are drawn from a couple of different perspectives, and comments are made on how these diagrams can be related to the more conventional language of chemistry. 相似文献
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Kercel SW 《化学与生物多样性》2007,4(10):2369-2385
Everything in Rosen's work flows from the principle of 'closure to efficient cause', the necessary and sufficient distinguishing feature of complexity, and a necessary distinguishing feature of an organism. Some students of Rosen find considerable confusion over the meaning of 'closure to efficient cause'. Such confusion is unnecessary. The matter is entirely cleared up by the (M,R)-system, a set of three algebraic maps. Each map must include one of the others in its co-domain, and is itself in the co-domain of the remaining map. Structurally, the three maps form a circular hierarchy of containment. This peculiar structure is Rosen's closure. Since each map represents an efficient cause, they reveal the character of efficient cause. The efficient cause of a process is represented as its 'dynamical law', and is a constraint that arises from the intersection of the morphology of the process and the inherent constraints in reality represented by the 'laws of Nature'. A critical, observable property (evidently unnoticed by Rosen), entailed by the closure, is its inherent ambiguity. From a foundation of ambiguity, the bizarre properties of complexity (e.g., non-computability, non-fractionability, undecidability, and incompleteness) follow in a straightforward manner, often with proofs simpler than those that Rosen discovered. 相似文献
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Edmonds B 《化学与生物多样性》2007,4(10):2386-2395
This paper is a critical recasting of some of Robert Rosen's thought. It is argued that a lot of the thrust of Rosen's work can be better understood when recast in terms of the context dependency of causal models. When recast in this way, I seek to highlight how his thought does not lead to the abandonment of formal modelling and a descent into relativism, but a more careful and rigours science of complex systems. This also sheds light on several aspects of modelling, including the need for multiple models, the nature of modelling noise, and why adaptive systems cause particular problems to modellers. In this way, I hope to decrease researchers fear that, by taking Rosen's criticisms seriously, they would have to abandon the realm of acceptable science. 相似文献
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Witten TM 《化学与生物多样性》2007,4(10):2332-2344
I have the pleasure to present a number of personal experiences that I had with Robert Rosen, both as his student and as a research colleague, and I will describe how this affected my academic career over the past decades. As a matter of fact, Rosen's work with (M,R)-systems as well as his continuing mentorship guided me into my own research in gerontology and geriatrics. Amazingly, this still continues to affect my work in complexity theory after 30 years. 相似文献
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Pattee HH 《化学与生物多样性》2007,4(10):2272-2295
The modeling relation and models of complex systems expressed by non-integrable constraints were developed during ca. 1970-1987, when I worked most closely with Robert Rosen. I contrast the modeling relation within the organism itself as a necessary condition for life and evolution, as Rosen developed it in his fundamental work 'Anticipatory Systems', with the modeling relation within our brain as a necessary condition for understanding life, as Rosen developed it in 'Life Itself'. Our approaches to the modeling relation were complementary. Rosen focused on the formal relational conditions necessary for life, and on the limitations that formal mathematical-symbol systems impose on our models. I focused on the physical conditions necessary for these abstract relations to be realized, and on the symbolic control in organisms that allows open-ended evolution. I contrast Rosen's views on physics and evolution in 'Anticipatory Systems' and later papers with his views in 'Life Itself', and I speculate on why they differ so greatly. 相似文献
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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. 相似文献
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Kier LB 《化学与生物多样性》2007,4(10):2473-2479
The work and inspiration of Robert Rosen is stated and expressed in personal tones. The concept of passages through water (H2O) near protein surfaces is reviewed in terms of its influence on ligand diffusion to an effector. This is offered as a target for interference by a non-specific general anesthetic agent. In view of the similarities between this anesthetic state and sleep, this mechanism is proposed to be operative for the sleep/wake states. Based on this mechanism and other factors, nitrogen (N2) is proposed as an exogenous sleep factor. 相似文献
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Topological patterns in the development and evolution of metazoa, from sponges to chordates, are considered by means of previously
elaborated methodology, with the genus of the surface used as a topological invariant. By this means metazoan morphogenesis
may be represented as topological modification(s) of the epithelial surfaces of an animal body. The animal body surface is
an interface between an organism and its environment, and topological transformations of the body surface during metazoan
development and evolution results in better distribution of flows to and from the external medium, regarded as the source
of nutrients and oxygen and the sink of excreta, so ensuring greater metabolic intensity. In sponges and some Cnidaria, the
increase of this genus up to high values and the shaping of topologically complicated fractal-like systems are evident. In
most Bilateria, a stable topological pattern with a through digestive tube is formed, and the subsequent topological complications
of other systems can also appear. The present paper provides a topological interpretation of some developmental events through
the use of well-known mathematical concepts and theorems; the relationship between local and global orders in metazoan development,
i.e., between local morphogenetic processes and integral developmental patterns, is established. Thus, this methodology reveals
a “topological imperative”: A certain set of topological rules that constrains and directs biological morphogenesis. 相似文献
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Defending Robert Rosen's claim that in every confrontation between physics and biology it is physics that has always had to give ground, it is shown that many of the most important advances in mathematics and physics over the last two centuries have followed from Schelling's demand for a new physics that could make the emergence of life intelligible. Consequently, while reductionism prevails in biology, many biophysicists are resolutely anti-reductionist. This history is used to identify and defend a fragmented but progressive tradition of anti-reductionist biomathematics. It is shown that the mathematico–physico–chemical morphology research program, the biosemiotics movement, and the relational biology of Rosen, although they have developed independently of each other, are built on and advance this anti-reductionist tradition of thought. It is suggested that understanding this history and its relationship to the broader history of post-Newtonian science could provide guidance for and justify both the integration of these strands and radically new work in post-reductionist biomathematics. 相似文献
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Robert Rosen's concept of (M,R)-systems was a fundamental advance in our understanding of the essential nature of a living organism as a self-organizing system, one that is closed to efficient causation, synthesizing, and maintaining all of the catalysts necessary for sustained operation during the whole period of its lifetime. Although it is not difficult to construct a model metabolic system to represent an (M,R)-system, such a model system will typically appear to lack organizational invariance, an essential property of a living (M,R)-system. To have this property, an (M,R)-system must not only be closed to external causation, it must also have its organization coded within itself, i.e., the knowledge of which components are needed for which functions must not be defined externally. In this paper, we discuss how organizational invariance may be achieved, and we argue that the apparent failure of previous models to be organizationally invariant is an artifact of the usual practice of treating catalytic cycles as 'black boxes'. If all of the steps in such a cycle are written as uncatalyzed chemical reactions, then it becomes clear that the organization of the system is fully defined by the chemical properties of the molecules that compose it. 相似文献
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The relational structure of RNA, DNA, and protein bears an interesting similarity to the determination problem in category
theory. In this paper, we present this deep-structure similarity and use it as a springboard for discussing some abstract
properties of coding in various systems. These abstract properties, in turn, may shed light on the evolution of the DNA world
from a semiotic perspective. According to the perspective adopted in this paper, living systems are not information processing
systems but “meaning-making” systems. Therefore, what flows in the genetic system is not “information” but “value.” We define
meaning, meaning-making, and value and then use these terms to explain the abstract dynamics of coding, which can illuminate many forms of sign-mediated activities
in biosystems. 相似文献
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《Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences》2013,44(2):199-207
The parts-based engineering approach in synthetic biology aims to create pre-characterised biological parts that can be used for the rational design of novel functional systems. Given the context-sensitivity of biological entities, a key question synthetic biologists have to address is what properties these parts should have so that they give a predictable output even when they are used in different contexts. In the first part of this paper I will analyse some of the answers that synthetic biologists have given to this question and claim that the focus of these answers on parts and their properties does not allow us to tackle the problem of context-sensitivity. In the second part of the paper, I will argue that we might have to abandon the notions of parts and their properties in order to understand how independence in biology could be achieved. Using Robert Cummins’ account of functional analysis, I will then develop the notion of a capacity and its condition space and show how these notions can help to tackle the problem of context-sensitivity in biology. 相似文献
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María Luz Cárdenas Claudio Gutierrez Jorge Soto-Andrade 《Journal of theoretical biology》2010,263(1):79-113
The major insight in Robert Rosen's view of a living organism as an (M,R)-system was the realization that an organism must be “closed to efficient causation”, which means that the catalysts needed for its operation must be generated internally. This aspect is not controversial, but there has been confusion and misunderstanding about the logic Rosen used to achieve this closure. In addition, his corollary that an organism is not a mechanism and cannot have simulable models has led to much argument, most of it mathematical in nature and difficult to appreciate. Here we examine some of the mathematical arguments and clarify the conditions for closure. 相似文献
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Michael Ruse 《Journal of the history of biology》2004,37(1):3-23
In his new book, The RomanticConception of Life: Science and Philosophyin the Age of Goethe, Robert J. Richardsargues that Charles Darwin's trueevolutionary roots lie in the German Romanticbiology that flourished around thebeginning of the nineteenth century. It isargued that Richards is quite wrong in thisclaim and that Darwin's roots are in theBritish society within which he was born,educated, and lived. 相似文献