Article

'Gloom in the society of enzymes': On the nature of biological information

Authors:
  • (Retired) Aragon Health Sciences Institute
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Abstract

Most approaches to information pay attention only to the 'positive' or constructive side ('presence') of this phenomenon: its composition, construction rules, emergence, effective activity, etc. However, the 'negative' or degrading aspects ('absences', disappearance of activity) are equally important within most biologico-informational processes. In fact, protein degradation can be put on a par with protein synthesis concerning its functionality and sophistication. By taking into account recent integrative discoveries in the molecular biology of the cell (signalling system, cell cycle, apoptosis, protein degradation, enzyme function) a wider approach encompassing both the 'presence' and 'absence' aspects seems possible. The overall dynamics which emerges--involving symmetry breaking and symmetry restoration by means of information processing mechanisms--may be extrapolated to neuronal and socio-economic realms too. Interestingly, the phenomenon of 'absence' can also be pinpointed, at least as a metaphor, within the internal structure of natural numbers.

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... During evolutionary transformations the isozymes acquire a specificity to different substrates that are similar in structure. The gradients of dynamic information are generated in a metabolic network at the multiple symmetry-breakings within the overall network of "wet symmetries" (Marijuán, 1996). Functional voids appearing in the system (in this case, they are deviations from normal trajectories) will precondition the complication of the structure and of the informational capacity of the system, and, in systems capable of evolutionary growth, filling in such voids is an emergent self-generating process. ...
... Besides metabolic bifurcations, the processes of protein degradation and apoptosis become informationally determined (programmed) within hypercycles. Appearing functional voids (Marijuán, 1996) become an important precondition for the development and informational growth within the system. Internalization of a void becomes possible because of the parallel process of genetic recombination. ...
Book
This book discusses the basic foundations of theoretical biology. Contrary to the objects of theoretical physics, the biological object contains a kind of ontological duality and refers to a fundamental wholeness of a living system. The rational interpretation of wholeness is considered by the author as a true basis for fundamental principles of development of theoretical biology and for understanding its link to physics, to psychology, and to semiotics. The rational holistic approach in application to theoretical biology can be substantiated through the clarification of internal logic of organization and description of biological systems. This logic will provide an understanding of the place of life in the Universe. The main goal of this book is to introduce the view that in the potentially infinite system of human knowledge, a proper clarification of the place of Man in the Universe is possible only via understanding of the phenomenon of life.
... During evolutionary transformations the isozymes acquire specificity to different substrates that are similar in structure. The gradients of dynamic information are generated in metabolic network at the multiple symmetry-breakings within the overall network of 'wet symmetries' (Marijuán, 1996b). Functional voids appearing in the system (in this case they are deviations from normal trajectories) precondition the complication of structure and of informational capacity of the system, and, in systems capable of evolutionary growth, filling in such voids is an emergent selfgenerating process. ...
... Appearing functional voids (Marijuán, 1996a) become an important precondition of the development and informational growth within the system. Internalization of a void becomes possible because of the parallel process of genetic recombination . ...
Article
Biological organization is based on the coherent energy transfer allowing for macromolecules to operate with high efficiency and realize computation. Computation is executed with virtually 100% efficiency via the coherent operation of molecular machines in which low-energy recognitions trigger energy-driven non-equilibrium dynamic processes. The recognition process is of quantum mechanical nature being a non-demolition measurement. It underlies the enzymatic conversion of a substrate into the product (an elementary metabolic phenomenon); the switching via separation of the direct and reverse routes in futile cycles provides the generation and complication of metabolic networks (coherence within cycles is maintained by the supramolecular organization of enzymes); the genetic level corresponding to the appearance of digital information is based on reflective arrows (catalysts realize their own self-reproduction) and operation of hypercycles. Every metabolic cycle via reciprocal regulation of both its halves can generate rhythms and spatial structures (resulting from the temporally organized depositions from the cycles). Via coherent events which percolate from the elementary submolecular level to organismic entities, self-assembly based on the molecular complementarity is realized and the dynamic informational field operating within the metabolic network is generated.
... There is a further and more 'positive' side to 'negative' information. Marijuan [23] conceptualized absences, needs, voids, etc. as instances of symmetry breaking in the trajectory of a life cycle. He noted that most approaches to information pay attention only to the 'positive' or constructive side ('presences') of a phenomenon: its composition, construction rules, emergence, effective, that is actual activity, etc. ...
... There is a further and more 'positive' side to 'negative' information. Marijuan (1996) sees absences, needs, voids, etc. as necessary to provide a complete picture of the infosphere. This concept goes back to the views of McLuhan of "negativity" and the subtle economy involved in predominantly signaling by "absences". ...
Article
The recent history of information theory and science shows a trend in emphasis from quantitative measures to qualitative characterizations. In parallel, aspects of information are being developed, for example by Pedro Marijuan, Wolfgang Hofkirchner and others that are extending the notion of qualitative, non-computational information in the biological and cognitive domain to include meaning and function. However, there is as yet no consensus on whether a single acceptable definition or theory of the concept of information is possible, leading to many attempts to view it as a complex, a notion with varied meanings or a group of different entities. In my opinion, the difficulties in developing a Unified Theory of Information (UTI) that would include its qualitative and quantita-tive aspects and their relation to meaning are a consequence of implicit or explicit reliance on the principles of standard, truth-functional bivalent or multivalent logics. In reality, information processes, like those of time, change and human con-sciousness, are contradictory: they are regular and irregular; consistent and inconsistent; continuous and discontinuous. Since the indicated logics cannot accept real contradictions, they have been incapable of describing the multiple but interre-lated characteristics of information. The framework for the discussion of information in this paper will be the new extension of logic to real complex processes that I have made, Logic in Reality (LIR), which is grounded in the dualities and self-dualities of quantum physics and cos-mology. LIR provides, among other things, new interpretations of the most fundamental metaphysical questions present in discussions of information at physical, biological and cognitive levels of reality including, especially, those of time, continuity vs. discontinuity, and change, both physical and epistemological. I show that LIR can constitute a novel and general ap-proach to the non-binary properties of information, including meaning and value. These properties subsume the notion of semantic information as well-formed, meaningful and truthful data as proposed most recently by Luciano Floridi. LIR sup-ports the concept of ‘biotic’ information of Stuart Kauffmann, Robert Logan and their colleagues and that of meaningful information developed by Christophe Menant. Logic in Reality does not pretend to the level of rigor of an experimental or mathematical theory. It is proposed as a meth-odology to assist in achieving a minimum scientific legitimacy for a qualitative theory of information. My hope is that by seeing information, meaning and knowledge as dynamic processes, evolving according to logical rules in my extended sense of logic, some of the on-going issues on the nature and function of information may be clarified.
... Although proteasomes are big multimeric complexes (on the order of 2 Megadalton, almost half the size of a ribosome) they passed unnoticed until the 90's. Very scant theoretical reflection has been devoted to the analysis of the cellular creative destruction that necessarily accompanies the constructive mechanisms of ribosomes and dynamically balances them (Marijuán, 1996). Again, most of the aspects distinguishable in this property have a top-down nature, and they are usually performed and orchestrated from the highest levels of cellular organization. ...
Article
This work explores a new understanding of informational phenomena based on the molecular organization of life. One of the central ideas is that the interrelationship among the recently framed fields of genomics, proteomics, and signaling science (crucial elements of the bioinformatic whole enterprise) may provide fundamental aspects of a new information synthesis. Thus, the new knowledge gained on the functionality and “existential flow” of the phenotypic molecular elements (basically the production and degradation of constituent enzymes and proteins—the transient proteome of the cell), which is intimately coupled with the intrinsic dynamics of the “DNA world” and with the communicational events stemming from the cell environment, could represent a microcosm for the whole in-formation phenomena. The variant in-formation spelling emphasizes that the cellular coupling among constitutive (proteomic), generative (genomic), and communicational (signaling) information genera produces a differentiated mode of existence, the living state, which is always in the making, perpetually in formation. The in-formability of the living supports the emergence of a completely new realm of ‘cognitive’ autonomous causality —and implies, in other regards, the emergence of meaning and of agency, and the foundation upon which far more complex, organismic, neuronal, and social events have been evolutionarily deployed. There follows a fundamental break with respect to the mechanistic chains of causality (and explanation) afforded by the reductionist vision. There is also, in this biological approach to informational phenomena, a compelling need for the development of a new communication theory of non-conservative nature. New logical principles are discussed which could guide biological systems in their inner choices between information ‘factories’ and information ‘garbage camps’. Finally, this bottom-up approach to the nature of information, molecular-biologically grounded as it is, does not militate against the top-down strategies. Conversely, it aims at a complementarity with germane conceptualizations that are currently being addressed in theoretical science, philosophy, neurosciences, and in social and technological disciplines.
... There is a further and more 'positive' side to 'negative' information. Marijuan (1996) sees absences, needs, voids, etc. as necessary to provide a complete picture of the infosphere. This concept goes back to the views of McLuhan of "negativity" and the subtle economy involved in predominantly signaling by "absences". ...
Article
Full-text available
The recent history of information theory and science shows a trend in emphasis from quantitative measures to qualitative characterizations. In parallel, aspects of information are being developed, for example by Pedro Marijuan, Wolf-gang Hofkirchner and others that are extending the notion of qualitative, non-computational information in the biological and cognitive domain to include meaning and function. However, there is as yet no consensus on whether a single acceptable definition or theory of the concept of information is possible, leading to many attempts to view it as a complex, a notion with varied meanings or a group of different entities. In my opinion, the difficulties in developing a Unified Theory of Information (UTI) that would include its qualitative and quantita-tive aspects and their relation to meaning are a consequence of implicit or explicit reliance on the principles of standard, truth-functional bivalent or multivalent logics. In reality, information processes, like those of time, change and human con-sciousness, are contradictory: they are regular and irregular; consistent and inconsistent; continuous and discontinuous. Since the indicated logics cannot accept real contradictions, they have been incapable of describing the multiple but interre-lated characteristics of information. The framework for the discussion of information in this paper will be the new extension of logic to real complex processes that I have made, Logic in Reality (LIR), which is grounded in the dualities and self-dualities of quantum physics and cos-mology. LIR provides, among other things, new interpretations of the most fundamental metaphysical questions present in discussions of information at physical, biological and cognitive levels of reality including, especially, those of time, continuity vs. discontinuity, and change, both physical and epistemological. I show that LIR can constitute a novel and general ap-proach to the non-binary properties of information, including meaning and value. These properties subsume the notion of semantic information as well-formed, meaningful and truthful data as proposed most recently by Luciano Floridi. LIR sup-ports the concept of 'biotic' information of Stuart Kauffmann, Robert Logan and their colleagues and that of meaningful information developed by Christophe Menant. Logic in Reality does not pretend to the level of rigor of an experimental or mathematical theory. It is proposed as a meth-odology to assist in achieving a minimum scientific legitimacy for a qualitative theory of information. My hope is that by seeing information, meaning and knowledge as dynamic processes, evolving according to logical rules in my extended sense of logic, some of the on-going issues on the nature and function of information may be clarified. Despite the widely varying content of theories of information, their emphasis has been on the quantitative aspects of information and their mathematical, abstract and essentially passive charac-ter, although information frequently involves human agents as active senders and receivers (Van Benthem & Van Rooy, 2003).This paper, however, focuses on the qualitative, causal properties of information. The framework for discussion will be my new extension of logic to real complex proc-esses, Logic in Reality (LIR) (Brenner, 2008). In my view, information is a phenomenon which, like human consciousness and change, instantiates real contradictions. LIR, in contrast to standard logics, is capable of describing such contradictions in physical, biological and cognitive processes, permitting stable inferences about them. The next Section 1 indicates some current approaches to the definition of information and of a unified theory of information. I proceed in Section 2 with an overview of LIR as a complete but non-standard logic, including its categorial ontology. In Section 3, I will propose an LIR philosophy of information, without pretending that it is a complete or unified theory. In Sections 4-7, different con-cepts of information are analyzed from the LIR perspective.
... Although proteasomes are big multimeric complexes (on the order of 2 Megadalton, almost half the size of a ribosome) they passed unnoticed until the 90's. Very scant theoretical reflection has been devoted to the analysis of the cellular creative destruction that necessarily accompanies the constructive mechanisms of ribosomes and dynamically balances them (Marijuán, 1996). Again, most of the aspects distinguishable in this property have a top-down nature, and they are usually performed and orchestrated from the highest levels of cellular organization. ...
Article
Full-text available
This work explores a new understanding of informational phenomena based on the molecular organization of life. One of the central ideas is that the interrelationship among the recently framed fields of genomics, proteomics, and signaling science (crucial elements of the bioinformatic whole enterprise) may provide fundamental aspects of a new information synthesis. Thus, the new knowledge gained on the functionality and "existential flow" of the phenotypic molecular elements (basically the production and degradation of constituent enzymes and proteins—the transient proteome of the cell), which is intimately coupled with the intrinsic dynamics of the "DNA world" and with the communicational events stemming from the cell environment, could represent a microcosm for the whole in-formation phenomena. The variant in-formation spelling emphasizes that the cellular coupling among constitutive (proteomic), generative (genomic), and communicational (signaling) information genera produces a differentiated mode of existence, the living state, which is always in the making, perpetually in formation. The in-formability of the living supports the emergence of a completely new realm of 'cognitive' autonomous causality —and implies, in other regards, the emergence of meaning and of agency, and the foundation upon which far more complex, organismic, neuronal, and social events have been evolutionarily deployed. There follows a fundamental break with respect to the mechanistic chains of causality (and explanation) afforded by the reductionist vision. There is also, in this biological approach to informational phenomena, a compelling need for the development of a new communication theory of non-conservative nature. New logical principles are discussed which could guide biological systems in their inner choices between information 'factories' and information 'garbage camps'. Finally, this bottom-up approach to the nature of information, molecular-biologically grounded as it is, does not militate against the top-down strategies. Conversely, it aims at a complementarity with germane conceptualizations that are currently being addressed in theoretical science, philosophy, neurosciences, and in social and technological disciplines.
... The user of a biological processor has to positively intervene with a processor, while the results of intervention must be uncontrollable (Gunji, 1995). As a result, 'functional void' (Marijuan, 1996) or unexpected error (Kampis, 1996) appears which can be internalized within a system as bifurcation (Igamb erdiev, 1994). This process is non -computabl e, but it can be defined in the theory of in variants of transformations which is important to introduce in biology. ...
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Full-text available
Information processing is a main property which distinguishes life from inorganic matter. Its background is the recognition activity of biomacro‐molecules based on quantum non‐demolition measurements. Reflective arrows in the set of mappings appearing from quantum measurements do form a hypercyclic structure which realizes information transfer and allows a system to self‐reproduce and evolve. These arrows correspond to Goedel numbers created inside a system.
... As far as signals viewed from the local perspective is concerned, they never attain a complete self-consistency in the form of the global synchronization among themselves (Conrad, 1996). There always remains those signals that are going to generate the counteractions toward themselves again in the form of signals (Marijuan, 1996). Signals are always in disequilibrium when perceived from the local perspective (Matsuno, 1985(Matsuno, , 1989, and in the process of perpetual disequilibration (Gunji, 1995). ...
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Information is intrinsically about a physical phenomenon that precipitates a globally synchronous time internally, in sharp contrast to Newtonian physics in which the globally synchronous time is simply declared to be absolute from the outset as being a metaphysical entity. Both capacities of generative activity and prescriptive specification are evident in the physics of information addressing the construction of a globally synchronous time from locally asynchronous ones on the actual scene. Appraisal of a locally asynchronous time assigned to each local material configuration is practiced by focusing on the occurrence of signaling and communication on material grounds. In this regard, the Cartesian physics prior to Newtonian successor is perceptive enough to appreciate the significance of signaling and communication in the local perspective. Proper understanding of the issue of information can be accomplished only by ameliorating Newtonian interventions too much of a metaphysical flavor. Information requires and waits for resurrection of the Cartesian physics.
... This contrasting idea can give rise to a drastic change from a science that concentrates on ends to a science that focuses on progression. When Conrad (1983a) invokes the vertical scheme of information processing in biological systems this represents an indefinite interface between a focal level of the system and the level providing a context to that focal level (Salthe, 1990;Marijuan, 1996). Due to the emphasis of the vertical scheme, a system (lower level) cannot be separated from its environment (upper level). ...
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Endophysics ultimately deduces an indefinite interface between an object and an observer. Objects, given such an interface, cannot be distinguished from the measurement process used to identify them. Evolutionary processes comprising of emergent properties and adaptability are seen in a new light. The concept of indefiniteness and/or paradox appears on the surface to be based on the epistemological framework of the Cartesian cut. However, perpetual processes consisting of generation and resolution of paradoxes are beyond the epistemological framework of measurement. They lead to the notion of progression, which one can refer to as ontological (or inherent) measurement.
... Energy dissipation asynchronous with energy conservation on the global scale can thus extend its cohesion towards the outside because energy conservation is eventually observed in globally synchronous time. Then, the likelihood would arise that dissipation asynchronous with conservation could generate and enhance material organizations due to its cohesive capacity connecting between locally asynchronous activities in the making and a global synchronization in the products (Marijuan, 1996). Although electrostatic interactions exhibit cohesive capacity between particles with opposite electric charges, dissipation asynchronous with conservation could become possible only when an exogenous energy flow becomes big enough to disturb the frozen internalization of both the measuring and the measured energy flows. ...
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Time is intrinsically locally asynchronous, dynamic in itself, and self-organizing in having locally asynchronous time precipitate further asynchronous time while leaving behind globally synchronous time. The resulting global synchronism is skewed in locally asynchronous time, while being vertical to the effected globally synchronous time. Information is a dynamic attribute of time and can be represented as a skewed synchronism in locally asynchronous time. Information originates in the communication among asynchronous times of a local character.
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The work of Luciano Floridi lies at the interface of philosophy, information science and technology, and ethics, an intersection whose existence and significance he was one of the first to establish. His closely related concepts of a philosophy of information (PI), informational structural realism, information logic (IL), and information ethics (IE) provide a new ontological perspective from which moral concerns can be addressed, especially but not limited to those arising in connection with the new information and communication technologies. In this paper, I relate Floridi's approach to another novel perspective, namely, that of an extension of logic to complex real processes, including those of information production and transfer. This non-propositional, non-truth-functional logic (logic in reality (LIR)) is grounded in the fundamental dualism (dynamic opposition) inherent in energy and accordingly present at all levels of reality. The LIR description of the dynamics of processes and their evolution is relevant to what Floridi refers to as the possible non-linguistic aspects of information. It suggests answers to some of Floridi's “outstanding problems” in PI related to the ontological status of information and how it is used in cognition. Floridi's IL retains the formal structure of the doxastic and epistemic logics from which he correctly distinguishes it and is the basis for his conceptual PI. However, LIR fulfills Floridi's implied requirement that logic be regarded as a natural phenomenon dealing with other natural phenomena, recovering its original philosophical function. LIR provides a logical foundation for discussion of ethical questions based on kinds of information that complements IL. Both are reconsiderations of logic that, as Marijuan suggests, may be necessary for the advancement of information technology in an ethical direction (cf. also Brenner). IE focuses on entities as constituted by information in an overall strategy that generalizes the concept of moral agents. LIR and its related ontology naturalize critical aspects of Floridi's theses, especially, the moral value of being as such and a non-separable joint responsibility of individuals and groups. I compare IE to other current approaches to ethics and information technology (e.g., phenomenological and social constructivist). Ethical information is defined “ecologically” in process terms as reality in a physical space (cf. Floridi), with an intentional “valence,” positive and negative, in the morally valued interaction between producer and receiver. LIR is neither topic-neutral nor context independent and can support an ethics involving apparently contradictory perspectives (e.g., internalist and externalist). Ethics involves practical reasoning, and unlike standard logics, LIR supports Magnani's approach to abductive reasoning in rational moral decision making. The basis of moral responsibility and the consequent behavior of individuals involved in information and communications technologies is the same logical–metaphysical principle of dynamic opposition instantiated at other levels of reality. The way moral responsibilities are actively accepted (or not) by individuals supervenes on their primitive psychological structure, which in turn reflects an evolutionary development grounded in the fundamental dualism of the physical world. The paper concludes with some suggestions of areas of philosophical research, such as causality, identity, and the ontological turn, where convergence of the Floridi and LIR approaches might be envisaged. Their overall motivation is the same, namely, the development of strategies for reinforcing and increasing ethical sensitivity wherever possible. The ethical information concept outlined in the paper supports the function of IE, assigned to it by Floridi, of potentially determining what is right and what is wrong. KeywordsLogic-Reality-Non-separability-Ontology-Information-Dialectic-Structure-Realism-Morality-Ethics
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Molecular computers are information processing systems in which individual molecules play a vital functional role. This chapter discusses the simulation systems to comprehend the information processing capabilities of biological systems, to provide design guidance for molecular computers fabricated from bona fide molecular materials, or to serve as biologically motivated artificial intelligence systems. The effort to synthesize biomimetic or de novo molecular computing devices is an outgrowth of fundamental research in molecular and cellular biophysics, condensed-matter physics, polymer chemistry, neurophysiology, and computer science. Some major applications of molecular computing may involve the contribution of microphysical processes to information processing and control in biological cells, the dynamics of evolutionary processes, the development of new classes of chemical materials, a more precise concept of computation and the linkage between the structure and function of computing systems, and a broader concept of cognitive computation. As per the tradeoff principle, processes in which the biological systems perform well, such as pattern recognition and learning, cannot be efficiently automated in structurally programmable machines. To the extent that structurally nonprogrammable systems, in particular molecular computers, can be fabricated, it should make new inroads into the class of problems that can be efficiently automated. If they cannot be fabricated, the clear implication is that some human computational functions cannot be used for automation. In either case, the theoretical, experimental, or technical sides of molecular computing provide a new and more comprehensive framework for the comparative computational analysis of brain and machine.
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Once the stipulation of ceteris paribus, requiring that other conditions are equal, is removed, recognition as a capacity for distinguishing between before and after its own act naturally comes to the surface. Although it has been extremely successful in deciphering a wide variety of material processes, physics still succumbs to its methodological limitation originating in adopting ceteris paribus in one form or another. In contrast, biology is unique in allowing the capacity of recognition as a basic simple fact. Interaction free from any from of ceteris paribus yields internal agents of recognition that can do measurement internally. Internal measurement refers to the process of symbol specification taking place internally, instead of its manipulation as practiced in the scheme of equations of motion. Appreciation of the capacity for recognition or internal measurement set free from the condition of ceteris paribus provides the possibility of the biologicalization of physics.
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The question of how life emerged from inanimate matter is closely related to the more fundamental question, namely: What is life? Both issues yield novel insights when discussed in the light of thermodynamics. The model proposed here is based on a simple assumption, namely, that life began with the accidental assembly of a self-replicating molecule. From this assumption the emergence of life naturally follows, enabling a new understanding of evolution as a whole. The evolution of any type of self-replicating systems, even the simplest ones, is shown to be highly efficient in extracting, recording and processing information about the environment. A variety of related issues yield some surprising conclusions when discussed in the thermodynamic context. New processes of order-increase are pointed out, a novel measure of information is proposed, and Lamarckianism is proved to be inconsistent with thermodynamics. Recent works on biogenesis and evolution are critically reviewed.
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Biology has benefited from a number of analogies and metaphors, in its attempt to rationalize the hierarchical structure of life's manifestations. Oft-cited is the comparison of a living organism to a society. Phenomenological similitude between the two extremes of the biological spectrum - the microscale of the cell and the macroscale of socioecosystems - has become strikingly evident, with the recent accumulation of empirical information on the metabolic infrastructure of the living cell. From the universal perspective of 'physiological determinism' reciprocal (or symmetric) relations are apparent at both levels of complexity. Unification of the biological hierarchy may follow a similar epistemological course to that in contemporary physics.
Article
Before division, cells must ensure that they finish DNA replication, DNA repair and chromosome segregation. They do so by using feedback controls which can detect the failure to complete replication, repair or spindle assembly to arrest the progress of the cell cycle at one of three checkpoints. Failures in feedback controls can contribute to the generation of cancer.
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In the last few years a general model of cell cycle control has been established for all eukaryotic cells. Experiments from a variety of organisms and from a variety of experimental approaches have identified a protein kinase and its unstable regulatory subunit as the activator of mitosis; related molecules seem to be involved in the activation of chromosome replication. The identification of the biochemical components of these important regulatory pathways is providing several new insights into homeostatic and developmental control mechanisms in higher organisms.
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Cellular proteins are marked for selective degradation by their ligation to the polypeptide ubiquitin. Recent studies have revealed information on the mechanisms involved in the selection of proteins for ligation to ubiquitin and on the mode of degradation of ubiquitinated proteins. Much remains to be learned about the high selectivity of this degradation pathway. Recent evidence that the cell-cycle regulatory proteins, cyclins, are degraded by the ubiquitin pathway points the way to future challenges in ubiquitin research.
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In the theoretical scenarios of biology, new insights can be gained by the introduction of information-processing and artificial intelligence concepts, helping to organize the explanation of the many intra- and inter-cellular phenomena that molecular biology is accumulating. Enzymes contain some of the immediate clues; the whole informational processing of prokaryotic cells is another central subject of search. Additionally, prolonging the informational perspective of the cell, a significant parallel can be drawn between informational processes in biological, social and artificial intelligence systems. A more tangible definition of biological complexity and biological intelligence emerges.
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Living cells respond to their environment by means of an interconnected network of receptors, second messengers, protein kinases and other signalling molecules. This article suggests that the performance of cell signalling pathways taken as a whole has similarities to that of the parallel distributed process networks (PDP networks) used in computer-based pattern recognition. Using the response of hepatocytes to glucagon as an example, a procedure is described by which a PDP network could simulate a cell signalling pathway. This procedure involves the following steps: (a) a bounded set of molecules is defined that carry the signals of interest; (b) each of these molecules is represented by a PDP-type of unit, with input and output functions and connection weights corresponding to specific biochemical parameters; (c) a "learning algorithm" is applied in which small random changes are made in the parameters of the cell signalling units and the new network is then tested by a selection procedure in favour of a specific input-output relationship. The analogy with PDP networks shows how living cells can recognize combinations of environmental influences, how cell responses can be stabilized and made resistant to damage, and how novel cell signalling pathways might appear during evolution.
Article
Although most eukaryotic proteins are synthesized in the cytoplasm from mRNAs originating in the nucleus, many function in specialized compartments and must be specifically translocated co- or post-translationally. A variety of signals contained within the amino acid sequence guide these processes as well as direct turnover by different proteolytic schemes. Several properties of the mature protein are determined as a result of translocation and can serve as predictors of cellular localization.
Article
Proteolytic processing is a common and effective mechanism of physiological regulation. The basic principle is a conformational change induced in the protein precursor by the post-translational proteolytic cleavage of a specific peptide bond. The extension of earlier studies of model zymogens to more complex systems of physiological regulation, using methods of both protein chemistry and molecular biology, has enormously extended knowledge of the repertoire of proteolytic processing reactions and has contributed significantly to current studies of the structure, domain organization and evolution of proteins.
Article
In multicellular organisms, homeostasis is maintained through a balance between cell proliferation and cell death. Although much is known about the control of cell proliferation, less is known about the control of cell death. Physiologic cell death occurs primarily through an evolutionarily conserved form of cell suicide termed apoptosis. The decision of a cell to undergo apoptosis can be influenced by a wide variety of regulatory stimuli. Recent evidence suggests that alterations in cell survival contribute to the pathogenesis of a number of human diseases, including cancer, viral infections, autoimmune diseases, neurodegenerative disorders, and AIDS (acquired immunodeficiency syndrome). Treatments designed to specifically alter the apoptotic threshold may have the potential to change the natural progression of some of these diseases.
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The folding of polypeptides emerging from ribosomes was analysed in a mammalian translation system using firefly luciferase as a model protein. The growing polypeptide interacts with a specific set of molecular chaperones, including Hsp70, the DnaJ homologue Hsp40 and the chaperonin TRiC. The ordered assembly of these components on the nascent chain forms a high molecular mass complex that allows the cotranslational formation of protein domains and the completion of folding once the chain is released from the ribosome.
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Internal quantum non-demolition measurements are inherent for biological organization and determine the essential features of living systems. Low energy dissipation in these measurements provided by slow conformational relaxation of biomacromolecular complexes (regarded as measuring devices) is the main precondition of enzyme operation and information transfer determining the steady non-equilibrium state of biosystems. The presence of an internal formal description inside a biosystem, expressed in genetic structures (developmental program), is a consequence of its quantum properties. Incompleteness of this formal description provides the possibility of the generation of new functional relations and interconnections inside the system. This is a logical precondition of an evolutionary process. The quantum mechanical uncertainty that underlies the appearance of bifurcations is considered to be the main physical foundation of complication and irreversible transformation of biosystems.
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There has been a deluge of reports, in this journal and elsewhere, dealing with the subject of signal transduction and the Ras protein. Why all the fuss? The following is a News and Views article with a difference - an explanation for those not close to events, and a celebration of an achievement in biomedical research.
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Molecular computers are natural or artificial systems in which macromolecules individually mediate critical information-processing functions. Biological organisms are the naturally occurring examples. Their information-processing virtuosity traces ultimately to the fact that macromolecules, most notably proteins, can recognize specific molecular objects in their environment in a manner that uses shape and depends sensitively on physiochemical context. The ultimate capabilities of this shape-based mode of computing and the technological implications that this mode may have are discussed. Basic principles of molecular computing are introduced and some ways that they might combine to yield new approaches to information technology are considered. Specifically, signal-integrating, optomolecular and neuromolecular computer architectures are described
Information and symmetry in the cellular system
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The origins of the nervous system
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Cell as a molecular computer (MCC)
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Computing with biological metaphors — some conceptual issues
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Enzymes, automata and artificial cells
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