Hylomorphism and the Metabolic Closure Conception of Life

This paper examines three exemplary theories of living organization with respect to their common feature of defining life in terms of metabolic closure: autopoiesis, (M, R) systems, and chemoton theory. Metabolic closure is broadly understood to denote the property of organized chemical systems that each component necessary for the maintenance of the system is produced from within the system itself, except for an input of energy. It is argued that two of the theories considered—autopoiesis and (M, R) systems—participate in a hylomorphist pattern of thinking which separates the “form” of the living system from its “matter.” The analysis and critique of hylomorphism found in the work of the philosopher Gilbert Simondon is then applied to these two theories, and on the basis of this critique it is argued that the chemoton model offers a superior theory of minimal life which overcomes many of the problems associated with the other two. Throughout, the relationship between hylomorphism and the understanding of living things as machines is explored. The paper concludes by considering how hylomorphism as a background ontology for theories of life fundamentally influences the way life is defined.     

On the origin of life event

On the assumption of a uniform sample space probability hypothesis it is estimated a maximum number of polypeptides (or other kind of polymers) that could be synthesized in the prebiotic Earth. Besides, on the basis of five premises that are postulated as indispensable requirements for the origin of a living system, under the constraints of a protein-nucleic acid chemistry, it is concluded categorically that the origin of life event could not be the result of unbiased polymerization phenomena. On the contrary, biased and specific patterns of polymerization had to be an essential component in this fundamental event.Finally, several theories on the origin of life and complementary concepts like hypercyclic organization and self-organization phenomena in dissipative structures are discussed in the light of the conclusions arrived at in this work.     

Physico-chemical and evolutionary constraints for the formation and selection of first biopolymers: towards the consensus paradigm of the abiogenic origin of life

During the last two decades, the common school of thought has split into two, so that the problem of the origin of life is tackled in the framework of either the 'replication first' paradigm or the 'metabolism first' scenario. The first paradigm suggests that the life started from the spontaneous emergence of the first, supposedly RNA-based 'replicators' and considers in much detail their further evolution in the so-called 'RNA world'. The alternative hypothesis of 'metabolism first' derives the life from increasingly complex autocatalytic chemical cycles. In this work, we emphasize the role of selection during the pre-biological stages of evolution and focus on the constraints that are imposed by physical, chemical, and biological laws. We try to demonstrate that the 'replication first' and 'metabolism first' hypotheses complement, rather than contradict, each other. We suggest that life on Earth has started from a 'metabolism-driven replication'; the suggested scenario might serve as a consensus scheme in the framework of which the molecular details of origin of life can be further elaborated. The key feature of the scenario is the participation of the UV irradiation both as driving and selecting forces during the earlier stages of evolution.     

Catalytic RNA and the origin of genetic systems

The recent discovery of catalytic RNA molecules has provoked enormous interest in the origin of life and has given rise to new speculations about how living systems developed on the primitive earth. Here we outline why the discovery of catalytic RNA molecules has profound evolutionary implications, and then go on to discuss models for the emergence of metabolic complexity and protein synthesis in a primitive 'RNA world', emphasizing the constraints imposed on such models by genetical arguments.     

Aspect-Object Alignment with Integer Linear Programming in Opinion Mining

Target extraction is an important task in opinion mining. In this task, a complete target consists of an aspect and its corresponding object. However, previous work has always simply regarded the aspect as the target itself and has ignored the important "object" element. Thus, these studies have addressed incomplete targets, which are of limited use for practical applications. This paper proposes a novel and important sentiment analysis task, termed aspect-object alignment, to solve the "object neglect" problem. The objective of this task is to obtain the correct corresponding object for each aspect. We design a two-step framework for this task. We first provide an aspect-object alignment classifier that incorporates three sets of features, namely, the basic, relational, and special target features. However, the objects that are assigned to aspects in a sentence often contradict each other and possess many complicated features that are difficult to incorporate into a classifier. To resolve these conflicts, we impose two types of constraints in the second step: intra-sentence constraints and inter-sentence constraints. These constraints are encoded as linear formulations, and Integer Linear Programming (ILP) is used as an inference procedure to obtain a final global decision that is consistent with the constraints. Experiments on a corpus in the camera domain demonstrate that the three feature sets used in the aspect-object alignment classifier are effective in improving its performance. Moreover, the classifier with ILP inference performs better than the classifier without it, thereby illustrating that the two types of constraints that we impose are beneficial.     

What is Life? Defining Life in the Context of Emergent Complexity

Erwin Schrödinger defined life not only as a “self-reproducing” aperiodic crystal of DNA coding for proteins but within the context of living entities increasing their order by dissipating matter/energy gradients to maintain themselves away from equilibirium. Since then most definitions of life have focused on the former. But living cells do more than replicate their DNA. Cells also have membrane barriers across which metabolites must move, via which energy transduction as well as information processing occurs, and within which metabolic transformation occurs. An approach of complex systems dynamics, including nonequilibrium thermodynamics, may provide a more robust approach for defining life than a “naked replicator” at the origin of life. The crucial issue becomes the process of emergence of life from pre-biotic chemistry, concomitant with the emergence of function, information, and semiosis. Living entities can be viewed as bounded, informed autocatalytic cycles feeding off matter/energy gradients, exhibiting agency, capable of growth, reproduction, and evolution. Understanding how life might have emerged should sharpen our definition of what life is.     

The origin of cellular life

This essay presents a scenario of the origin of life that is based on analysis of biological architecture and mechanical design at the microstructural level. My thesis is that the same architectural and energetic constraints that shape cells today also guided the evolution of the first cells and that the molecular scaffolds that support solid-phase biochemistry in modern cells represent living microfossils of past life forms. This concept emerged from the discovery that cells mechanically stabilize themselves using tensegrity architecture and that these same building rules guide hierarchical self-assembly at all size scales (Sci. Amer 278:48-57;1998). When combined with other fundamental design principles (e.g., energy minimization, topological constraints, structural hierarchies, autocatalytic sets, solid-state biochemistry), tensegrity provides a physical basis to explain how atomic and molecular elements progressively self-assembled to create hierarchical structures with increasingly complex functions, including living cells that can self-reproduce.     

In the Beginning was a Mutualism - On the Origin of Translation

The origin of translation is critical for understanding the evolution of life, including the origins of life. The canonical genetic code is one of the most dominant aspects of life on this planet, while the origin of heredity is one of the key evolutionary transitions in living world. Why the translation apparatus evolved is one of the enduring mysteries of molecular biology. Assuming the hypothesis, that during the emergence of life evolution had to first involve autocatalytic systems which only subsequently acquired the capacity of genetic heredity, we propose and discuss possible mechanisms, basic aspects of the emergence and subsequent molecular evolution of translation and ribosomes, as well as enzymes as we know them today. It is possible, in this sense, to view the ribosome as a digital-to-analogue information converter. The proposed mechanism is based on the abilities and tendencies of short RNA and polypeptides to fold and to catalyse biochemical reactions. The proposed mechanism is in concordance with the hypothesis of a possible chemical co-evolution of RNA and proteins in the origin of the genetic code or even more generally at the early evolution of life on Earth. The possible abundance and availability of monomers at prebiotic conditions are considered in the mechanism. The hypothesis that early polypeptides were folding on the RNA scaffold is also considered and mutualism in molecular evolutionary development of RNA and peptides is favoured.     

Organisation de la phase minérale chez Vaceletia crypta (Vacelet)Démosponge,Sphinctozoaire actuelle. Comparaison avec des formes aragonitiques du Trias de Turquie

The fundamental microstructural and ultrastructuralcaracteristics of a non fibrous carbonate tissue has been revealed by the study of the only living Sphinctozoa: Vaceletia crypta (Vacelet), Demospongia.These observations yield important data for interpretation of homogeneous carbonate structure in the skeleton of some fossil sponges. Effectively, we notice that two triassic forms, morphologically very different (Sphinctozoa and Inozoa) show remarkable microstructural analogies with Vaceletia crypta. These considerations should not be leaved out to establish an only classification of Sponges, joining both living and fossil forms.Moreover, the elementary skeletal constituants ofthe two forms show dimensions which indicate a growth in size in comparison with the living species. This increase has probably a diagenetic origin (adjunction of aragonite). So it appears that the present aspect of the mineral components cannot result from a reduction in size (micritization), as has been sometimes asserted.     

Could Work Be a Source of Behavioural Disorders? A Study in Horses

Stress at work, as shown by a number of human studies, may lead to a variety of negative and durable effects, such as impaired psychological functioning (anxiety, depression…). Horses share with humans this characteristic of working on a daily basis and are submitted then to work stressors related to physical constraints and/or more “psychological” conflicts, such as potential controversial orders from the riders or the requirement to suppress emotions. On another hand, horses may perform abnormal repetitive behaviour (“stereotypies”) in response to adverse life conditions. In the present study, we investigated whether the type of work the horses are used for may have an impact on their tendency to show stereotypic behaviour (and its type) outside work. Observations in their box of 76 horses all living in the same conditions, belonging to one breed and one sex, revealed that the prevalence and types of stereotypies performed strongly depended upon the type of work they were used for. The stereotypies observed involved mostly mouth movements and head tossing/nodding. Work constraints probably added to unfavourable living conditions, favouring the emergence of chronic abnormal behaviours. This is especially remarkable as the 23 hours spent in the box were influenced by the one hour work performed every day. To our knowledge, this is the first evidence of potential effects of work stressors on the emergence of abnormal behaviours in an animal species. It raises an important line of thought on the chronic impact of the work situation on the daily life of individuals.     

Life under minimal energy expenses

Vital activity is impossible without energy. Lung ventilation, heart activity, digestion, secretion, locomotion--these functions require and consume a substantial amount of energy. But preservation of viability requires comparatively small amount of energy, and in some cases can manage almost without energy. A prolonged preservation of viability with minimal energy consumption we conventionally call life without energy. This special feature of living organisms is considered in the present work in a comparative physiological aspect.     

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.     

生命机体危险因子信息特征分析

旨在生命机体与危险因子间建立生命物质信息对话平台,以物质化的信息,或信息化的物质的思维进行理解和推论,建立物质承载信息,信息通过物质的形式传递的思维模式,对生命信息中危险因子的属性、分类以及生命机体对危险因子的识别方式进行分析,从以上两个方面不同角度阐述危险因子与生命机体机制信息的相关互动关系。在分析与解读的过程中,主张建立合乎自然生成逻辑的科学概念,而摒弃一些主观是非逻辑所推导建立起来的概念,还原生命物质和生命过程的本来生物学位置及性质;主张一元化的思考方式和整体性理解生命信息安全控制机制的核心部分。分析结果:就生命信息中危险因子的属性和分类进行了分析,指出危险因子具有生命信息属性和生命安全属性两个属性,依据危险因子物质来源的不同,分外源性和内源性两类,绘出危险因子来源分类汇总图;从机体方面对危险因子识别方式不同,分为PRR识别方式和抗原(样)受体识别方式两类,并绘出危险因子识别方式分类汇总图。综合危险因子的属性、分类和生命机体对危险因子的识别方式,绘制出危险因子与生命机体机制信息的相关互动图,从保守性结构信息、生理产物信息、对机体损伤信息、代谢通路信息、对机体变应信息、精细纯外观构象信息及内在性核心信息7个方面对两者的相互关系进行了引证和分析,进一步阐释了生命信息安全控制机制。     

Necessity,Futility and the Possibility of Defining Life are all Embedded in its Origin as a Punctuated-gradualism

The criteria used for defining life are influenced by various philosophical visions about life, ranging from holism to reductionism and from mechanistic-reductionism to vitalism. Using different scenarios about the origin and evolution of life as well as properties of energy-dissipative systems, artificial life simulations and basic tenets of xenobiology, guidelines can be established for formulating a definition of life. A definition of life is proposed that is parametric, non-Earth-centric, quantitative and capable of discriminating ‘living entities’ from ‘life’. Living entities are defined as self-maintained systems, capable of adaptive evolution individually, collectively or as a line of descend. Life is a broader concept indicating that the capacity to express these attributes is either virtual or actual. At least four major phase transitions can be recognized during the origin of life (reflexive activity; self-regulated homeostasis; the advent of informatons and the origin of adaptive evolution); these make the origin and evolution of early life an example of ‘punctuated gradualism’. Such phase transitions can be used to identify a boundary in early evolution where life began. This contribution identifies the step in the evolution of a dynamic system when digital control of the system’s state becomes dominant over analogical control, and genetic information is irreversibly used for adaptive evolution, as the boundary between non-living and living systems.     

Homeotic proteins participate in the function of human-DNA replication origins

Recent evidence points to homeotic proteins as actors in the crosstalk between development and DNA replication. The present work demonstrates that HOXC13, previously identified as a new member of human DNA replicative complexes, is a stable component of early replicating chromatin in living cells: it displays a slow nuclear dynamics due to its anchoring to the DNA minor groove via the arginine-5 residue of the homeodomain. HOXC13 binds in vivo to the lamin B2 origin in a cell-cycle-dependent manner consistent with origin function; the interaction maps with nucleotide precision within the replicative complex. HOXC13 displays in vitro affinity for other replicative complex proteins; it interacts also in vivo with the same proteins in a cell-cycle-dependent fashion. Chromatin-structure modifying treatments, disturbing origin function, reduce also HOXC13–origin interaction. The described interactions are not restricted to a single origin nor to a single homeotic protein (also HOXC10 binds the lamin B2 origin in vivo). Thus, HOX complexes probably contribute in a general, structure-dependent manner, to origin identification and assembly of replicative complexes thereon, in presence of specific chromatin configurations.     

What could arsenic bacteria teach us about life?

In this paper, I discuss the recent discovery of alleged arsenic bacteria in Mono Lake, California, and the ensuing debate in the scientific community about the validity and significance of these results. By situating this case in the broader context of projects that search for anomalous life forms, I examine the methodology and upshots of challenging biochemical constraints on living things. I distinguish between a narrower and a broader sense in which we might challenge or change our knowledge of life as the result of such a project, and discuss two different kinds of projects that differ in their potential to overhaul our knowledge of life. I argue that the arsenic bacteria case, while potentially illuminating, is the kind of constraint-challenging project that could not—in spite of what was said when it was presented to the public—change our knowledge of life in the deeper sense.