Towards synthetic cells:are cells computers making computers?

Understanding life supposes that one will,one day,reconstruct cells. A deep analysis of what life is shows that a cell is similar to a computers making computer. This asks for several orginal levels of organisation. First,the cell needs to be seen as a machine separated from the genetic program,which it runs. Over generations the machine reproduces,while the program replicates. Reproduction is a process which is able to accumulate valuable information over generations. Extracting valuable information from an ocean of noise requires an energy-dependent process which uses energy to prevent degradation of functional entities. Analysis of bacterial genomes shows that the core set of genes which persist in most genomes code for the functions needed to perform this process of ratchet-like information accumulation. It also suggests that a mineral,polyphosphates,could be a ubiquitous (and stable) energy source essential for the process.     

Life, self-reproduction and information: beyond the machine metaphor

The problem of representing information in automation models of self-replication is considered. It is shown that, unlike in the natural reproduction process, in a computable model the reproduced entities do not contain all the information necessary for guiding the process. Current theoretical understanding of life and its replication, based on such models, is argued to be essentially inadequate. The solution to this problem is claimed to require recognition of the theoretical fact that information in living systems is different from that subsumed under the category of "knowledge", which is representable as computer programs or triggers of state transitions. A discussion of fundamentals of a new theory of information and its relationship to replication models is given and a new direction of further developments of biological theories is envisioned.     

Bacteria as computers making computers

Various efforts to integrate biological knowledge into networks of interactions have produced a lively microbial systems biology. Putting molecular biology and computer sciences in perspective, we review another trend in systems biology, in which recursivity and information replace the usual concepts of differential equations, feedback and feedforward loops and the like. Noting that the processes of gene expression separate the genome from the cell machinery, we analyse the role of the separation between machine and program in computers. However, computers do not make computers. For cells to make cells requires a specific organization of the genetic program, which we investigate using available knowledge. Microbial genomes are organized into a paleome (the name emphasizes the role of the corresponding functions from the time of the origin of life), comprising a constructor and a replicator, and a cenome (emphasizing community-relevant genes), made up of genes that permit life in a particular context. The cell duplication process supposes rejuvenation of the machine and replication of the program. The paleome also possesses genes that enable information to accumulate in a ratchet-like process down the generations. The systems biology must include the dynamics of information creation in its future developments.     

A Representational Similarity Analysis of the Dynamics of Object Processing Using Single-Trial EEG Classification

The recognition of object categories is effortlessly accomplished in everyday life, yet its neural underpinnings remain not fully understood. In this electroencephalography (EEG) study, we used single-trial classification to perform a Representational Similarity Analysis (RSA) of categorical representation of objects in human visual cortex. Brain responses were recorded while participants viewed a set of 72 photographs of objects with a planned category structure. The Representational Dissimilarity Matrix (RDM) used for RSA was derived from confusions of a linear classifier operating on single EEG trials. In contrast to past studies, which used pairwise correlation or classification to derive the RDM, we used confusion matrices from multi-class classifications, which provided novel self-similarity measures that were used to derive the overall size of the representational space. We additionally performed classifications on subsets of the brain response in order to identify spatial and temporal EEG components that best discriminated object categories and exemplars. Results from category-level classifications revealed that brain responses to images of human faces formed the most distinct category, while responses to images from the two inanimate categories formed a single category cluster. Exemplar-level classifications produced a broadly similar category structure, as well as sub-clusters corresponding to natural language categories. Spatiotemporal components of the brain response that differentiated exemplars within a category were found to differ from those implicated in differentiating between categories. Our results show that a classification approach can be successfully applied to single-trial scalp-recorded EEG to recover fine-grained object category structure, as well as to identify interpretable spatiotemporal components underlying object processing. Finally, object category can be decoded from purely temporal information recorded at single electrodes.     

Concepts of rational taxonomy

The problems are discussed related to development of concepts of rational taxonomy and rational classifications (taxonomic systems) in biology. Rational taxonomy is based on the assumption that the key characteristic of rationality is deductive inference of certain partial judgments about reality under study from other judgments taken as more general and a priory true. Respectively, two forms of rationality are discriminated--ontological and epistemological ones. The former implies inference of classifications properties from general (essential) properties of the reality being investigated. The latter implies inference of the partial rules of judgments about classifications from more general (formal) rules. The following principal concepts of ontologically rational biological taxonomy are considered: "crystallographic" approach, inference of the orderliness of organismal diversity from general laws of Nature, inference of the above orderliness from the orderliness of ontogenetic development programs, based on the concept of natural kind and Cassirer's series theory, based on the systemic concept, based on the idea of periodic systems. Various concepts of ontologically rational taxonomy can be generalized by an idea of the causal taxonomy, according to which any biologically sound classification is founded on a contentwise model of biological diversity that includes explicit indication of general causes responsible for that diversity. It is asserted that each category of general causation and respective background model may serve as a basis for a particular ontologically rational taxonomy as a distinctive research program. Concepts of epistemologically rational taxonomy and classifications (taxonomic systems) can be interpreted in terms of application of certain epistemological criteria of substantiation of scientific status of taxonomy in general and of taxonomic systems in particular. These concepts include: consideration of taxonomy consistency from the standpoint of inductive and hypothetico-deductive argumentation schemes and such fundamental criteria of classifications naturalness as their prognostic capabilities; foundation of a theory of "general taxonomy" as a "general logic", including elements of the axiomatic method. The latter concept constitutes a core of the program of general classiology; it is inconsistent due to absence of anything like "general logic". It is asserted that elaboration of a theory of taxonomy as a biological discipline based on the formal principles of epistemological rationality is not feasible. Instead, it is to be elaborated as ontologically rational one based on biologically sound metatheories about biological diversity causes.     

Sexualité des patients après traitements anti-cancéreux-nécessité d'une prévention

Sex and cancer, pleasure and death are words very difficult and painful to associate and to evoke. The sexuality of patients with cancerous diseases is unrecognized by physicians and very little present in the practice of sexology. the sexual life of cancerous patients must be preserved. The preventions must have aims, means and time. The aims are: to allow, to keep, to find or to rediscover a sexual and relational life. The means are:

? systematic information on the clinical reality and his results,

? directed information on the sexual reality and his capacities,

? thinked information on the sense and the value of the sexuality and of the pleasure.

The time is before, during and after the treatment for cancer. The prevention is also sexological treatments if sexuals symptoms occur.     

At the dawn of a new revolution in life sciences

In a recently published article Sydney Brenner argued that the most relevant scientific revolution in biology at his time was the breakthrough of the role of "information" in biology.The fundamental concept that integrates this new biological "information" with matter and energy is the universal Turing machine and von Neumann's self-reproducing machines.In this article we demonstrate that in contrast to Turing/von Neumann machines living cells can really reproduce themselves.Additionally current knowledge on the roles of noncoding RNAs indicates a radical violation of the central dogma of molecular biology and opens the way to a new revolution in life sciences.     

A FORTRAN computer program for storage and retrieval of personal journal references

A FORTRAN program is described for interactive maintenance of a personal library of journal references and reprints. The program queries the user for category (author, journal, year, title, and keyword) information during entry of new documents. Retrieval of documents in the set is accomplished by entering as many search words as desired, in any order, and in any category. The program returns documents that match for all entered words. Other functions include terminal display of the information stored for a given document and the ability to generate an alphabetized bibliographic listing from among the document set. A correction routine and a routine for listing the contents of the search word files are also included.     

论婴儿类别形成的过程

文章简要回顾了婴儿类别形成中的知觉类别和概念类别之争,提出了婴儿类别形成阶段的假设：知觉类别与概念类别的形成是同一个过程。类别形成和概念形成是同时发生的两个不同阶段。婴儿类别的形成是建立诊断标准的过程,而概念形成是信息分析的过程,并且概念的形成影响类别的形成。     

The Chinese family as instituted fantasy: or,rescuing kinship imaginaries from the ‘symbolic’

This article revisits well‐travelled ethnographic portrayals of traditional Chinese family dynamics to draw attention to desire as a product of family life and to how crucial elements of family organization and ideology can be understood, in turn, as effects of desire – that is, as instituted fantasies. Although my case in point is the Chinese family, the analysis addresses the category ‘family’ cross‐culturally. In any of its variations, the ‘family’ exists at two synergistically implicated levels: first, it comprises an important part of the reality into which individuals are socialized; second, it embodies in instituted form individuals' attempts to realize – to bring into being – social arrangements as they would like them to be. In the Chinese case, at least two ironies are embedded in this synergy. First, women are primary producers and reproducers of the family in the ‘real world’, despite the fact that patriliny as ‘instituted fantasy’ downplays or veils their agency. Second, the normative subordination of the son to a patriarchal father, expressed and mediated through institutions including ancestor worship and valorization of filial piety, veils a valorizing of the son as agent or protagonist of filial action. Although ultimately unrealizable, patrilineal and familial fantasies animate Chinese family life and are thus an important constituent of Chinese realities. To these ends the analysis re‐purposes ‘the symbolic’ and ‘imaginaries’, categories widely employed in contemporary gender studies and social theory, arguing that understanding kinship enjoins incorporating desire's role both in defining institutions and in motivating their creators.     

Role of Utility and Inference in the Evolution of Functional Information

Functional information means an encoded network of functions in living organisms from molecular signaling pathways to an organism’s behavior. It is represented by two components: code and an interpretation system, which together form a self-sustaining semantic closure. Semantic closure allows some freedom between components because small variations of the code are still interpretable. The interpretation system consists of inference rules that control the correspondence between the code and the function (phenotype) and determines the shape of the fitness landscape. The utility factor operates at multiple time scales: short-term selection drives evolution towards higher survival and reproduction rate within a given fitness landscape, and long-term selection favors those fitness landscapes that support adaptability and lead to evolutionary expansion of certain lineages. Inference rules make short-term selection possible by shaping the fitness landscape and defining possible directions of evolution, but they are under control of the long-term selection of lineages. Communication normally occurs within a set of agents with compatible interpretation systems, which I call communication system. Functional information cannot be directly transferred between communication systems with incompatible inference rules. Each biological species is a genetic communication system that carries unique functional information together with inference rules that determine evolutionary directions and constraints. This view of the relation between utility and inference can resolve the conflict between realism/positivism and pragmatism. Realism overemphasizes the role of inference in evolution of human knowledge because it assumes that logic is embedded in reality. Pragmatism substitutes usefulness for truth and therefore ignores the advantage of inference. The proposed concept of evolutionary pragmatism rejects the idea that logic is embedded in reality; instead, inference rules are constructed within each communication system to represent reality, and they evolve towards higher adaptability on a long time scale.     

Species: the concept, category and taxon

The term species by itself is vague because it refers to the species concept, the species category and the species taxon, all of which are distinct although related to one another. The species concept is not primarily a part of systematics, but has always been an integral part of basic biological theory, It is based on evolutionary theory and applies only to sexually reproducing organisms. The species concept and the phyletic lineage concept are quite distinct although they are related to one another. The important aspect of the species concept is lack of gene flow between different species, and hence the defining criterion of the species is genetic isolation. The species concept is often considered as non‐dimensional, both in time and space. Species possess three different major properties, namely genetic isolation, reproductive isolation and ecological isolation; these properties evolve at different times and under the effect of different causes during the speciation process. Speciation requires an external isolating barrier during the initial allopatric phase in which genetic isolation evolves and must reach 100% efficiency. The subsequent sympatric phase of speciation occurs after the disappearance of the external isolating barrier when members of the two newly evolved species can interact with one another and exert mutual selective demands on one another. Much of the reproductive and ecological isolation evolves during this secondary sympatric phase. The species category is a rank in the taxonomic hierarchy and serves as the basis on which the diversity of organisms is described; it is not the same as the species concept. The species category applied to all organisms, sexually and asexually reproducing. The species taxon is the practical application of the species category in systematics with the recognition of species taxa requiring many arbitrary decisions. No single set of rules exist by which the species category can be applied to all organisms. Recognition of species taxa in asexually reproducing organisms is based on amount of variation and gaps in the variation of phenotypic features associated with ecological attributes of these organisms as compared with similar attributes in sympatric species taxa of sexually reproducing organisms. Species taxa are multidimensional in that they exist over space–time and often have fuzzy borders. Because recognition of species taxa, including those in sexually reproducing organisms, depends on many arbitrary decisions especially when dealing with broad geographical and temporal ranges, species taxa cannot be used as the foundation for developing and testing theoretical concepts in evolutionary theory which can only be done with the non‐dimensional species concept.     

A systematic quality assurance framework for the upgrade of radiation oncology information systems

In spite of its importance, no systematic and comprehensive quality assurance (QA) program for radiation oncology information systems (ROIS) to verify clinical and treatment data integrity and mitigate against data errors/corruption and/or data loss risks is available. Based on data organization, format and purpose, data in ROISs falls into five different categories: (1) the ROIS relational database and associated files; (2) the ROIS DICOM data stream; (3) treatment machine beam data and machine configuration data; (4) electronic medical record (EMR) documents; and (5) user-generated clinical and treatment reports from the ROIS. For each data category, this framework proposes a corresponding data QA strategy to very data integrity. This approach verified every bit of data in the ROIS, including billions of data records in the ROIS SQL database, tens of millions of ROIS database-associated files, tens of thousands of DICOM data files for a group of selected patients, almost half a million EMR documents, and tens of thousands of machine configuration files and beam data files. The framework has been validated through intentional modifications with test patient data. Despite the ‘big data’ nature of ROIS, the multiprocess and multithread nature of our QA tools enabled the whole ROIS data QA process to be completed within hours without clinical interruptions. The QA framework suggested in this study proved to be robust, efficient and comprehensive without labor-intensive manual checks and has been implemented for our routine ROIS QA and ROIS upgrades.     

VisiCoor: A simple program for visualization of proteins

A well-drawn picture acts as an excellent metaphor for something real, and human vision provides instant, random access to any part of which the picture represents. It is in this sense that pictures can convey information more effectively than words alone. The power of the graphics work-stations available today makes visual presentation of scientific results a reality. A molecular graphics program for investigating protein structures, as well as several sample plots that show the power of the program, are presented.     

WELLBEING,SCHIZOPHRENIA AND EXPERIENCE MACHINES

In the USA and England and Wales, involuntary treatment for mental illness is subject to the constraint that it must be necessary for the health or safety of the patient, if he poses no danger to others. I will argue against this necessary condition of administering treatment and propose that the category of individuals eligible for involuntary treatment should be extended. I begin by focusing on the common disorder of schizophrenia and proceed to demonstrate that it can be a considerable harm to a person's life without causing the person to be a danger to himself. I illuminate this claim by constructing a thought experiment concerning a person who slips on a banana peel and falls into a malfunctioning version of Robert Nozick's experience machine. I propose that the reasons why we should remove the person from the machine are the same reasons why we should administer involuntary treatment to individuals with schizophrenia. I rebut three objections to the analogy and conclude that if we believe that we have a duty to provide treatment for reasons relating to a person's wellbeing, it follows that we should reject the health or safety requirement and instead broaden the category of individuals who are eligible for involuntary treatment.     

A simple model based on the first principles

A simple model based on the first principles is proposed, which describes the reduplication of a molecular structure as a sequence of stages with probabilities that can be estimated on the basis of the general theory of molecular transformations. It is demonstrated that the reproduction of genetic information in time (life phenomenon) over a long period is impossible without the simultaneous "death effect". Taking into account the peculiarities of transient states (quantum beats) leads to the appearance of self-oscillations.