Is it Useful to Have a Clear-cut Definition of Life? On the Use of Fuzzy Logic in Prebiotic Chemistry

Many scientists, including one of the authors of the present paper, have devoted time to try to find a definition for life (Bersini and Reisse 2007). It is clear that a consensus will never be reached but, more importantly, it seems that the issue itself could be without major interest. It is indeed impossible to define a “natural” frontier between non-living and living systems and therefore also impossible to define dichotomic criteria which could be used in order to classify systems in one of these two classes (living or non-living). Fuzzy logic provides a natural way to deal with problems where class membership lacks sharply defined criteria. It also offers the possibility to avoid losing time with unnecessary controversies such as deciding whether a virus is, or is not, a living system.     

Towards a General Definition of Life

A new definition of life is proposed and discussed in the present article. It is formulated by modifying and extending NASA’s working definition of life, which postulates that life is a “self-sustaining chemical system capable of Darwinian evolution”. The new definition includes a thermodynamical aspect of life as a far from equilibrium system and considers the flow of information from the environment to the living system. In our derivation of the definition of life we have assumed the hypothesis, that during the emergence of life evolution had to first involve autocatalytic systems that only subsequently acquired the capacity of genetic heredity. The new proposed definition of life is independent of the mode of evolution, regardless of whether Lamarckian or Darwinian evolution operated at the origins of life and throughout evolutionary history. The new definition of life presented herein is formulated in a minimal manner and it is general enough that it does not distinguish between individual (metabolic) network and the collective (ecological) one. The newly proposed definition of life may be of interest for astrobiology, research into the origins of life or for efforts to produce synthetic or artificial life, and it furthermore may also have implications in the cognitive and computer sciences.

     

A physical characterization of biological information and communication system model of ecosystems

What is information for living organisms? An answer to this question is given on a physical basis and a contrast between genetic information and sensory information is stressed with a relation to information theory. A simple model of an environment of living organisms is investigated on the basis of communication systems model proposed by the author and a cost of information transmission is taken into consideration through capacity cost theory. It is shown that channel capacity of information theory can be interpreted as an environment, and furthermore that a large diversity of genetic messages needs a large capacity of the environment. In addition, a definition of life in terms of information is proposed and a unified view on life processes is suggested.     

Complexity, communication between cells, and identifying the functional components of living systems: Some observations

The concept of complexity has become very important in theoretical biology. It is a many faceted concept and too new and ill defined to have a universally accepted meaning. This review examines the development of this concept from the point of view of its usefulness as a criteria for the study of living systems to see what it has to offer as a new approach. In particular, one definition of complexity has been put forth which has the necessary precision and rigor to be considered as a useful categorization of systems, especially as it pertains to those we call living. This definition, due to Robert Rosen, has been developed in a number of works and involves some deep new concepts about the way we view systems. In particular, it focuses on the way we view the world and actually practice science through the use of the modelling relation. This mathematical object models the process by which we assign meaning to the world we perceive. By using the modelling relation, it is possible to identify the subjective nature of our practices and deal with this issue explicitly. By so doing, it becomes clear that our notion of complexity and especially its most popular manifestations, is in large part a product of the historical processes which lead to the present state of scientific epistemology. In particular, it is a reaction to the reductionist/mechanistic view of nature which can be termed the Newtonian Paradigm. This approach to epistemology has dominated for so long that its use as a model has become implicit in most of what we do in and out of science. The alternative to this approach is examined and related to the special definition of complexity given by Rosen. Some historical examples are used to emphasize the dependence of our view of what is complex in a popular sense on the ever changing state of our knowledge. The role of some popular concepts such as chaotic dynamics are examined in this context. The fields of artificial life and related areas are also viewed from the perspective of this rigorous view of complexity and found lacking. The notion that in some way life exists at the edge of chaos is examined from the perspective of the second law of thermodynamics given by Schneider and Kay. Finally, the causal elements in complex systems are explored in relation to complexity. Rosen has shown that a clear difference in causal relations exists between complex and simple systems and that this difference leads to a uniquely useful definition of what we mean by living. Rosen makes it very clear that the class of systems which are complex is a much larger class than those which we call living. For that reason, the focus of this review will be on complexity as a stepping stone towards the deeper question of what makes a system alive.     

Three-dimensional finite element analysis of glenoid replacement prostheses: a comparison of keeled and pegged anchorage systems

Glenoid component loosening is the dominant cause of failure in total shoulder arthroplasty. It is presumed that loosening in the glenoid is caused by high stresses in the cement layer. Several anchorage systems have been designed with the aim of reducing the loosening rate, the two major categories being "keeled" fixation and "pegged" fixation. However, no three-dimensional finite element analysis has been performed to quantify the stresses in the cement or to compare the different glenoid prosthesis anchorage systems. The objective of this study was to determine the stresses in the cement layer and surrounding bone for glenoid replacement components. A three-dimensional model of the scapula was generated using CT data for geometry and material property definition. Keeled and pegged designs were inserted into the glenoid, surrounded by a 1-mm layer of bone cement. A 90 deg arm abduction load with a full muscle and joint load was applied, following van der Helm (1994). Deformations of the prosthesis, stresses in the cement, and stresses in the bone were calculated. Stresses were also calculated for a simulated case of rheumatoid arthritis (RA) in which bone properties were modified to reflect that condition. A maximum principal stress-based failure model was used to predict what quantity of the cement is at risk of failure at the levels of stress computed. The prediction is that 94 percent (pegged prosthesis) and 68 percent (keeled prosthesis) of the cement has a greater than 95 percent probability of survival in normal bone. In RA bone, however, the situation is reversed where 86 percent (pegged prosthesis) and 99 percent (keeled prosthesis) of the cement has a greater than 95 percent probability of survival. Bone stresses are shown to be not much affected by the prosthesis design, except at the tip of the central peg or keel. It is concluded that a "pegged" anchorage system is superior for normal bone, whereas a "keeled" anchorage system is superior for RA bone.     

Is there a "molecular Nirvana Principle"? Towards a unified resolutional model of the biological symbol-matter dichotomy

In the present paper, the metapsychological "Nirvana Principle" is investigated evolutionarily at the earliest forms of life in a highly tentative way. A corresponding "molecular Nirvana Principle" is proposed, where the recent suggestions of the "internal measurement" biophysical quantum-molecular research programme of modern quantum biology are introduced, in relation to the former metapsychological theory, conceived to be valid in the entire realm of living systems (just as it was intended by the original author). By an appropriate introduction of a special primordeal dynamical time inversion symmetry breaking, originating in a premeval self-measurement in a composite nucleic acid-protein system, a special internal symmetry restoration time series is defined. In this way, a strictly physically defined self-identity ("molecular Nirvana," special physical symmetry restored) is derived, which is put equal to the quantum physical equivalent and root of the goals of evolutionarily higher level fundamental drives (the "Nirvana Principle"). It is shown that it is a natural requirement that the following internal regressive time (-reversal) physical molecular relations (and so the ultimate time symmetry) is mapped onto space, as is also suggested by some symbol-theoretical propositions.     

Origins for Everyone

The origin of life on Earth remains a mystery, but the question can still be approached with scientific rigor. Identifying life??s origins requires the definition of life itself, which has been described as a self-sustaining system capable of Darwinian evolution, although it's also possible that there is no good scientific definition. All known living systems contain linear strings of information based on DNA, a molecule that makes Darwinian evolution possible through replication and mutation. This review explains the scientific concepts and issues underlying the origin of life, possible mechanisms of origins, and the features of living systems that can arguably be viewed as an inevitable consequence of the earliest molecules.     

Evolution,reproduction and definition of life

Synthetic theory of evolution is a superior integrative biological theory. Therefore, there is nothing surprising about the fact that multiple attempts of defining life are based on this theory. One of them even has a status of NASA’s working definition. According to this definition, ‘life is a self-sustained chemical system capable of undergoing Darwinian evolution’ Luisi (Orig Life Evol Bios 28:613–622, 1998); Cleland, Chyba (Orig Life Evol Bios 32:387–393, 2002). This definition is often considered as one of the more theoretically mature definitions of life. This Darwinian definition has nonetheless provoked a lot of criticism. One of the major arguments claims that this definition is wrong due to ‘mule’s problem’. Mules (and other infertile hybrids), despite being obviously living organisms, in the light of this definition are considered inanimate objects. It is strongly counterintuitive. The aim of this article was to demonstrate that this reasoning is false. In the later part of the text, I also discuss some other arguments against the Darwinian approach to defining life.     

Autopoiesis 40 years Later. A Review and a Reformulation

The concept of autopoiesis was proposed 40 years ago as a definition of a living being, with the aim of providing a unifying concept for biology. The concept has also been extended to the theory of knowledge and to different areas of the social and behavioral sciences. Given some ambiguities of the original definitions of autopoiesis, the concept has been criticized and has been interpreted in diverse and even contradictory ways, which has prevented its integration into the biological sciences where it originated. Here I present a critical review and conceptual analysis of the definition of autopoiesis, and propose a new definition that is more precise, clear, and concise than the original ones. I argue that the difficulty in understanding the term lies in its refined conceptual subtlety and not, as has been claimed by some authors, because it is a vacuous, trivial or very complex concept. I also relate the concept of autopoiesis to the concepts of closed systems, boundaries, homeostasis, self-reproduction, causal circularity, organization and multicellularity. I show that under my proposed definition the concept of a molecular autopoietic system is a good demarcation criterion of a living being, allowing its general integration into the biological sciences and enhancing its interdisciplinary use.     

Autogenesis: the evolution of replicative systems

Questions concerning the nature and origin of living systems and the hierarchy of their evolutionary processes are considered, and several problems which arise in connection with formerly developed theories--the autopoiesis of Maturana & Varela, the POL theory of Haukioja and the earlier developed evolutionary theory of Csányi--are discussed. The organization of living systems, the use of informational terms and the question how reproduction can enter into their characterization, problems of autonomy and identity are included in the list. It is suggested that replication--a copying process achieved by a special network of interrelatedness of components and component-producing processes that produces the same network as that which produced them--characterizes the living organization. The information "used" in this copying process, whether it is stored by special means or distributed in the whole system, is called replicative information. A theoretical model is introduced for the spontaneous emergence of replicative organization, called autogenesis. Autogenesis commences in a system by an organized "small" subsystem, referred to as AutoGenetic System Precursor (AGSP), which conveys replicative information to the system. During autogenesis, replicative information increases in system and compartment(s) form. A compartment is the co-replicating totality of components. The end state of autogenesis is an invariantly self-replicating organization which is unable to undergo further intrinsic organizational changes. It is suggested that replicative unities--such as living organisms--evolve via autogenesis. Levels of evolution emerge as a consequence of the relative autonomy of the autogenetic unities. On the next level they can be considered as components endowed with functions and a new autogenetic process can commence. Thus evolution proceeds towards its end state through the parallel autogenesis of the various levels. In terms of applications, ontogenesis is dealt with in detail as an autogenetic process as is the autogenesis of the biosphere and the global system.     

Shades of irreplaceability: towards a measure of the contribution of sites to a reservation goal

In most regions there are many possible ways of combining numbers of sites into reserve systems that represent a range of natural feasures. The irreplaceability of a site is operationally defined as the percentage of these alternative systems in which it occurs. This is a fundamental measure of the conservation value of the site in terms of its potential contribution to the achievement of a reservation goal or, alternatively, the options for reservation that are lost if the site is lost. The measure allows decisions to be made on the future of individual sites in the context of their value, in combination with other sites, to the conservation of the full range of natural features in a region. It also provides a logical framework for the design of whole systems of reserves, with decisions proceeding from the most to the least irreplaceable. Irreplaceability can be measured directly for small data sets but must be predicted for regional data sets. A promising approach to prediction is discussed that requires validation with more extensive trials. The irreplaceability of a site depends on a specific reservation target and changes as some of the site's features become progressively represented in reserves elsewhere. The concept of irreplaceability undermines notions of conservation value that are static or based on a single static system of sites to achieve a reservation goal.     

Bimolecular systems: I. Linear systems of complexes

A vast number of biologically important processes are based upon bimolecular systems. In these systems intermediate complexes are formed. Bimolecular systems in which no complex-complex interactions occur are called linear systems of complexes. A definition and some characteristic properties of these systems are given here. There may exist a contradiction of Onsager's principle of detailed balancing in these systems; however, no principal differences are found between the steady state behavior of an open system and that of a closed system. It is shown that the steady state behavior of a linear system of complexes of arbitrary complexity has some similarities with the steady state behavior of a simple bimolecular system, e.g., Michaelis-Menten enzymatic reaction. Multiplicity of action of the substances participating in biomolecular processes may produce some qualitative differences in the steady state behavior of the system.     

The "near zone" effect in dynamic chaos

The dynamics of the system with a determined chaotic behavior (Lorentz system) was studied by comparing the histograms. It was shown that the dynamics of the system exhibits phenomena similar to those observed in studies of fluctuations in physical systems. In particular, upon comparison of histograms constructed from different time intervals, the "near zone" effect makes itself evident. It was shown that a very slight modulation of only one parameter of the system leads to a change in behavior.     

Identification and characterization of "basal" Ca2+-independent Mg2+-dependent ATP-hydrolase enzymatic activity in smooth muscle cell plasma membrane fractions

It is shown, that for correct definition of "basal" Ca(2+)-independent Mg(2+)-dependent ATPase ac-activity (10-13 mmol Pi/hour on 1 mg of protein) in a fraction of uterus smooth muscle cell plasma membranes is necessary to use in medium without calcium of an incubation not only EGTA and digitonin--of the factor of infringement in activity by this subcellular structure, but inhibitors of others Mg(2+)-dependent ATP-hydrolyse enzymatic systems localized as in plasma membrane (Na+, K(+)-ATPase) and in others subcellular frames, first of all, in mitochondria (Mg(2+)-ATPase) and endoplasmic reticulum (transport Ca2+, Mg(2+)-ATPase). In the case of a sacolemal fraction of a smooth muscle the contribution of others Mg(2+)-dependent ATP-hydrolyse systems in a common enzymatic hydrolysis ATP, which unconnected to functioning "basal" Ca(2+)-independent Mg(2+)-dependent ATPase, is very appreciable and achieves 35%. The researches, carried out in the frameworks of definition of initial velocity of enzymatic reaction, have enabled to define its some properties--cationic and anionic specificity, and also sensitivity to action of some inhibitors. It has appeared, that the "basal" Ca(2+)-independent Mg(2+)-dependent ATP-hydrolyse reaction is nonspecific rather both in relation to cations of divalent metals Me2+, and cations of monovalent metals and anions, which were utilized for support of ionic strength. The cations La--antagonist of cations Ca--practically did not influence enzymatic activity. The non-specific inhibitors transport of ATPases--p-chloromercuribenzoate, o-vanadate and eosine Y with a various degree of efficiency inhibited "basal" Ca(2+)-independent Mg(2+)-dependent ATP-hydrolyse reaction. On the basis of the analysis of the own and literary data the conclusion is made that "basal" Ca(2+)-independent Mg(2+)-dependent ATPase of a smooth muscle cell plasma membrane is considerably less sensitive to action of nonspecific inhibitors of the Ca(2+)-transporting systems, than these systems.     

Finding one of a kind: advances in single-protein production

An ultimate goal for any protein production system is to express only the protein of interest without producing other cellular proteins. To date, there are only two established methods that will allow the successful expression of only the protein of interest: the cell-free in vitro protein synthesis system and the in vivo single-protein production (SPP) system. Although single-protein production can be achieved in cell-free systems, it is not easy to completely suppress the production of cellular proteins during the production of a protein of interest in a living cell. However, the finding of a unique sequence-specific mRNA interferase in Escherichia coli led to the development of the SPP system by converting living cells into a bioreactor that produces only a single protein of interest without producing any cellular proteins. This technology not only provides a new high expression system for proteins, but also offers a novel avenue for protein structural studies.     

A Universal Definition of Life: Autonomy and Open-Ended Evolution

Life is a complex phenomenon that not only requires individual self-producing and self-sustaining systems but also a historical-collective organization of those individual systems, which brings about characteristic evolutionary dynamics. On these lines, we propose to define universally living beings as autonomous systems with open-ended evolution capacities, and we claim that all such systems must have a semi-permeable active boundary (membrane), an energy transduction apparatus (set of energy currencies) and, at least, two types of functionally interdependent macromolecular components (catalysts and records). The latter is required to articulate a 'phenotype-genotype' decoupling that leads to a scenario where the global network of autonomous systems allows for an open-ended increase in the complexity of the individual agents. Thus, the basic-individual organization of biological systems depends critically on being instructed by patterns (informational records) whose generation and reliable transmission cannot be explained but take into account the complete historical network of relationships among those systems. We conclude that a proper definition of life should consider both levels, individual and collective: living systems cannot be fully constituted without being part of the evolutionary process of a whole ecosystem. Finally, we also discuss a few practical implications of the definition for different programs of research.     

Confrontation of the Cybernetic Definition of a Living Individual with the Real World

The cybernetic definition of a living individual proposed previously (Korzeniewski, 2001) is very abstract and therefore describes the essence of life in a very formal and general way. In the present article this definition is reformulated in order to determine clearly the relation between life in general and a living individual in particular, and it is further explained and defended. Next, the cybernetic definition of a living individual is confronted with the real world. It is demonstrated that numerous restrictions imposed on the cybernetic definition of life by physical reality imply a number of particular properties of life that characterize present life on Earth, namely: (1) a living individual must be a dissipative structure (and therefore a low-entropy thermodynamic system out of the state of equilibrium); (2) spontaneously-originated life must be based on organic compounds; (3) evolutionarily stable self-dependent, free-living individuals must have some minimal level of complexity of structure and function; (4) a living individual must have a record of identity separated from an executive machinery; (5) the identity of living individuals must mutate and may evolve; (6) living individuals may collect and accumulate information in subsequent generations over very long periods of time; (7) the degree of complexity of a living individual reflects the degree of complexity of its environment (ecological niche) and (8) living individuals are capable of supple adaptation to varying environmental conditions. Thus, the cybernetic definition of a living individual, when confronted with the real physical world, generates most of the general properties of the present life on Earth.     

Defining ‘Life’

There is no broadly accepted definition of life. Suggested definitions face problems, often in theform of robust counter-examples. Here we use insights fromphilosophical investigations into language to argue thatdefining `life' currently poses a dilemma analogous to thatfaced by those hoping to define `water' before the existenceof molecular theory. In the absence of an analogous theoryof the nature of living systems, interminable controversyover the definition of life is inescapable.     

On analogous systems

A precise definition is given for the analogy of a dynamical system to another system (or subsystem thereof). It is shown that there exist systems which are universal in the sense that they contain subsystems analogous to any arbitrary dynamical system. From this it is argued that the identification of system properties in physics and biology has only a conventional and subjective character, rather than the objective character which is usually supposed. Some preliminary implications of this view are discussed.     

Robustness: confronting lessons from physics and biology

The term robustness is encountered in very different scientific fields, from engineering and control theory to dynamical systems to biology. The main question addressed herein is whether the notion of robustness and its correlates (stability, resilience, self‐organisation) developed in physics are relevant to biology, or whether specific extensions and novel frameworks are required to account for the robustness properties of living systems. To clarify this issue, the different meanings covered by this unique term are discussed; it is argued that they crucially depend on the kind of perturbations that a robust system should by definition withstand. Possible mechanisms underlying robust behaviours are examined, either encountered in all natural systems (symmetries, conservation laws, dynamic stability) or specific to biological systems (feedbacks and regulatory networks). Special attention is devoted to the (sometimes counterintuitive) interrelations between robustness and noise. A distinction between dynamic selection and natural selection in the establishment of a robust behaviour is underlined. It is finally argued that nested notions of robustness, relevant to different time scales and different levels of organisation, allow one to reconcile the seemingly contradictory requirements for robustness and adaptability in living systems.