Ontologies of living things are increasingly grounded on the concepts and practices of current life science. Biological development is a process, undergone by living things, which begins with a single cell and (in an important class of cases) ends with formation of a multicellular organism. The process of development is thus prima facie central for ideas about biological individuality and organismality. However, recent accounts of these concepts do not engage developmental biology. This paper aims to fill the gap, (...) proposing the lineage view of stem cells as an ontological framework for conceptualizing organismal development. This account is grounded on experimental practices of stem cell research, with emphasis on new techniques for generating biological organization in vitro. On the lineage view, a stem cell is the starting point of a cell lineage with a specific organismal source, time-interval of existence, and ‘tree topology’ of branch-points linking the stem to developmental termini. The concept of ‘enkapsis’ accommodates the cell-organism relation within the lineage view; this hierarchical notion is further explicated by considering the methods and results of stem cell experiments. Results of this examination include a (partial) characterization of stem cells’ developmental versatility, and the context-dependence of developmental processes involving stem cells. (shrink)

The Cell Ontology (CL) is designed to provide a standardized representation of cell types for data annotation. Currently, the CL employs multiple is_a relations, defining cell types in terms of histological, functional, and lineage properties, and the majority of definitions are written with sufficient generality to hold across multiple species. This approach limits the CL’s utility for cross-species data integration. To address this problem, we developed a method for the ontological representation of cells and applied this method (...) to develop a dendritic cell ontology (DC-CL). DC-CL subtypes are delineated on the basis of surface protein expression, systematically including both species-general and species-specific types and optimizing DC-CL for the analysis of flow cytometry data. This approach brings benefits in the form of increased accuracy, support for reasoning, and interoperability with other ontology resources. 104. Barry Smith, “Toward a Realistic Science of Environments”, Ecological Psychology, 2009, 21 (2), April-June, 121-130. Abstract: The perceptual psychologist J. J. Gibson embraces a radically externalistic view of mind and action. We have, for Gibson, not a Cartesian mind or soul, with its interior theater of contents and the consequent problem of explaining how this mind or soul and its psychological environment can succeed in grasping physical objects external to itself. Rather, we have a perceiving, acting organism, whose perceptions and actions are always already tuned to the parts and moments, the things and surfaces, of its external environment. We describe how on this basis Gibson sought to develop a realist science of environments which will be ‘consistent with physics, mechanics, optics, acoustics, and chemistry’. (shrink)

In 1877, the young Alfred Espinas defended a philosophical study, ‘doctorat ès lettres’, at the Sorbonne University, entitled Des Sociétés animales. This was to become one of the principal sources of French organicist sociology. The paradox, however, is that this work seems to be fundamentally a study of natural science. Espinas tried to justify his position theoretically through two types of reciprocally exclusive and uncomplementary arguments. The first one consists in showing that only certain kinds of animal groupings belong legitimately, (...) if not academically, to sociology. The second one has a greater audacious and uncontrollable dimension. It consists in asserting that all pluricellular organisms are true societies. In this article we first focus on the role played by cellular theory in such a ‘sociologization’ of biology, concerning the extension of sociology. Second, we examine the importance of such confusion within the fields of extension, in aiming to explain the conceptual transfers between social sciences and life sciences, in the second half of the 19th century. (shrink)

The cell theory of Schleiden and Schwann is generalized to the effect that throughout the natural world, in physics, biology, and sociopsychology, there is a widespread phenomenon of the existence of organized cells, whose organization is usually protected by barriers. These barriers exist not only in space, but in time and even in other domains. These barriers typically not only protect the organization within the cell from external disturbance, but they actively participate in reducing the internal disorganization. It (...) appears that the quantum phase cell or its equivalent, the discrete quantum state, may be a physical analog of the organized biological cell. The sampling and ambiguity theorems of communication theory throw new light on phase cells. The quantum phase cell has both configuration and momentum elements, which are analogous respectively to the somatic elements in the cytoplasm of a cell and the genetic elements in the DNA. A biological cell or organism, a physical quantum state, and a human being as a sociopsychological entity each has a natural individuality. A natural individuality is a somewhat mysterious thing, since in addition to specificity, it also involves stochasticity and complementarity. There are some striking and unexplained spin-analog characteristics in biology which have a relation to boson- and fermion-analog characteristics in biology that corresponds with the known relation in physics. The hypothesis suggested in our earlier paper, that quantum mechanical entropy is diminished in interaction, is clarified and sharpened in this paper. (shrink)

Despite recent progress in the identification of genes that regulate longevity, aging remains a mysterious process. One influential hypothesis is the idea that the potential for cell division and replacement are important factors in aging. In this work, we review and discuss this perspective in the context of interventions in mammals that appear to accelerate or retard aging. Rather than focus on molecular mechanisms, we interpret results from an integrative biology perspective of how gene products affect cellular functions, which (...) in turn impact on tissues and organisms. We review evidence suggesting that mutations that give rise to features resembling premature aging tend to be associated with cellular phenotypes such as increased apoptosis or premature replicative senescence. In contrast, many interventions in mice that extend lifespan and might delay aging, including caloric restriction, tend to either hinder apoptosis or result in smaller animals and thus may be the product of fewer cell divisions. Therefore, it appears plausible that changes in the number of times that cells, and particularly stem cells, divide during an organism's lifespan influence longevity and aging. We discuss possible mechanisms related to this hypothesis and propose experimental paradigms. BioEssays 30:567–578, 2008. © 2008 Wiley Periodicals, Inc. (shrink)

The author assumes that the biological evolution must reflect itself also in the energetic processes of the organism. Several concept are discussed, in view of a characterization of the energetic economy of the organism. Two of these are thought to have particular significance related to evolution: the energetic efficiency and the capacity for energetic production . E is the ratio of the performed useful work to the amount of energy “spent”; P is the ratio of the performed useful (...) work to the product of the mass of the living system and time. An evolution of both E and P during the animal phylogenesis is assumed. The evolution of E is generally evident at the level of more elementary metabolic processes, while that of P at the level of more complex functions or of the organism as a whole. In many cases, the increase of P is associated with a decrease of E. The main evolutionary feature of biological energetic economy is the increase of the capacity for energetic production. This holds true even if the increase of P can be achieved only at the expense of a reduction of the energetic efficiency, of a “waste” of energy, especially in the most highly developed systems of the organism.L'évolution biologique doit se refléter, selon l'avis de l'auteur, aussi dans les processus énergétiques de l'organisme. On discute quelques notions qui pourraient caractériser l'économie énergétique de celui-ci. Deux de celles-ci ont une signification évolutive particulière: le rendement énergétique et la capacité de production énergétique . E est le rapport du travail util effectué à la quantité d'énergie “dépensée”; P est le rapport du travail util effectué au produit de la masse du système vivant avec de le temps. L'auteur considère qu'il y a une évolution des deux grandeurs au cours de la phylogénèse animale. L'évolution d'E se manifeste spécialement au niveau des processus métaboliques élémentaires, tandis que celle de P au niveau des fonctions plus complexes ou de l'organisme entier. Dans beaucoup de cas, l'accroissement de P entraîne une diminution de E. Le trait évolutif principal de l'énergétique biologique c'est l'accroissement de la capacité de production énergétique, même si cela suppose une réduction du rendement, une “dissipation” d'énergie, surtout dans les systèmes les plus développés de l'organisme.Die biologische Evolution soll sich, nach dem Erachten des Verfassers, auch in den energetischen Vorgange des Organismus kundtun. Es werden einige Begriffe erörtert, welche den Energiehaushalt des Organismus kennzeichnen können. Zwei von diesen Begriffen haben eine besondere entwicklungsgeschichtliche Bedeutung: die energetische Leistung und das Vermögen zur Energieproduktion . E ist das Verhältnis der geleisteten nützlichen Arbeit zur verbrauchten Energiemenge; P ist das Verhältnis der nützlichen Arbeit zum Produkt von Masse des lebenden Systems und Zeit. Der Verfasser ist der Meinung, dass es eine Evolution von E und P während der tierischen Phylogenesis gäbe. Die Evolution von E äussert sich meist in der Ebene der elementaren metabolischen Vorgänge, hingegen die von P an komplexeren Funktionen. In zahlreichen Fällen, vermindert E während P wächst. Die evolutive Grundzug der biologischen Energetik ist das Anwachsen der Fähigkeit zur Energieproduktion, sogar wenn dieses nur auf Kosten einer Verminderung der energetischen Leistung, einer „Vergeudung“ der Energie verwirklichen kann. (shrink)

What general conclusions can be drawn about the reception of zymase, its relation to the larger shift from a protoplasm to an enzyme theory of life, and its status as a social phenomenon?The most striking and to me unexpected pattern is the close correlation between attitude toward zymase and professional background. The disbelief of the fermentation technologists, Will, Delbrück, Wehmer, and even Stavenhagen, was as sharp and unanimous as the enthusiasm of the immunologists and enzymologists, Duclaux, Roux, Fernback, and (...) Bertrand, and of Pfeffer, the experimental plant physiologist. Other skeptics—Voit, Kupffer, and Fischer—were conservatives in traditional fields. In all these cases it seems clear that professional commitments and outlook profoundly influenced the reception of zymase.In some cases there is a correlation with a specific earlier statement favoring the protoplasm theory or predicting a fermentation enzyme. Reynolds Green is a striking case of both. In 1893 he stated his belief that life processes in higher plants and fungi were identical, both being mediated by protoplasm.109 Thus he claimed that digestion was not carried out by enzymes, as in higher animals, but by the whole protoplasm, and so too fermentation in yeast: “All the metabolic processes must be carried out in the unicellular organism in the same mass of protoplasm.”110 But Green also insisted that there was no essential difference between “organized” and “unorganized ferments”; enzymes were simply more highly differentiated and specialized forms of primitive protoplasm. He spoke of “the alcoholic ferment” (that is, enzyme), and of intracellular enzymes—very advanced beliefs for 1893. Thus it is understandable why Green saw no reason to doubt his first negative results with yeast juice, and rushed into print. But it is also understandable that he persisted and soon became an outspoken advocate of Buchner's view; like Wroblewski and Pfeffer, he had already accepted the idea of an intracellular fermentation enzyme.The physiological chemists also fit the pattern in a special way. Physiological chemistry is generally regarded as the source of biochemistry; indeed, many early biochemists were trained in physiological chemistry, and imbibed there a progressive interest in enzymes and metabolism. It is not surprising, therefore, that on the whole Neumeister, Madfadyen, Wroblewski, and Loew accepted cell-free fermentation. But what is surprising, and significant, is the diversity of opinion in this group, from Abeles' living protoplasm to Wroblewski's organized array of active proteins. The feelings of the physiological chemists were mixed, and there was enough of the old protoplasm view in Macfadyen's and even Wroblewski's views to allow Buchner to see them as attacks on zymase. The ideas of physiological chemistry were also changing; the idea of protoplasm was already adjusting to the new interest in enzymes in the early 1890's. But in contrast to immunochemistry, the change in physiological chemistry was gradual, uneven, undramatic, and relatively invisible. For the new biochemistry, the tradition of physiological chemistry was the source of traditional conservatism as well as of new ideas of enzymes.In general, then, I claim that it was not experimental facts that determined attitudes toward zymase so much as previous commitments, experience, and expectations. Initially, at least, zymase was less a determinant of opinion than a touchstone of pre-existing opinion. Like a prism, it revealed the spectrum of existing attitudes toward vital phenomena.Also relevant here is the fact that the experimental evidence was entirely ambiguous; the interpretation of Buchner's experiments with antiseptics or dried yeast depended entirely on how far one was willing to stretch the scope of the terms “protoplasm” and “enzyme”. Likewise, how important one judged the instability of zymase to be, or the low level of in vitro activity, depended largely on one's point of view. There was no crucial experiment, no certain proof. Logically zymase could be regarded as protoplasm. A. Fischer did so in 1900;111 Macfadyen was still wavering in 1907;112 and Beijerinck was holding out as late as 1916.113 There were undoubtedly others. Besides the special case of Reynolds Green and the technologists, there are no recorded cases of conversion.But if there was no evidence to convert a dedicated protoplasmist, there was plenty to encourage a dedicated belief in the enzyme theory, and that, I believe, is precisely what happened. The arguments of Buchner et al in support of zymase had the greatest effect not on the protoplasmists but on those who were already predisposed toward the biochemical view. The zymase debate enabled the emerging group of biochemists to recognizethemselves as a group with a community of out-look and objectives; it brought the issue of protoplasm vs. enzyme into the open and gave it a specific and concrete issue on which to turn. The debate sharpened the biochemists' awareness that their point of view was becoming the new mainstream of biochemical thought.All this of course had an important secondary effect on those who opposed the new view, or who were not immediately concerned with it. After the zymase debate, it would have been almost impossible to ignore the new ideas; the dramatic and wide publicity the debate enjoyed would have made it difficult not to take sides. Buchner's successful defense of zymase itself became an important influence on opinion; the new movement had to be looked at with respect. But the primary effect of the debate, I assert, was on those who were already inclined to the new view. The outcome was not a mass conversion of individuals, nor the ejection of one idea by another. The sides probably did not change much; the real change was in the way each side regarded itself and its place in history. The zymase debate may perhaps best be regarded as a process of selection. Buchner's party became aware of itself as the new progressive point of view, while those holding the traditional view could no longer expound it publicly without appearing obstinate or old-fashioned. Thus the way was clear for the gradually wider establishment of the new ideas, especially among the new generation of biochemists. In this specific sense, the acceptance of zymase was a social phenomenon.This way of looking at the zymase debate also illuminates its coincidence with the emergence of biochemistry as a profession. The new professional trappings and organizations were the social manifestation of the new self-awareness gained from the zymase controversy. One of the most important effects on those disposed toward the new view was the awareness of an intellectual community and of the need to give that community social forms. The almost mythical importance of Buchner's “victory” over the old protoplasm theory that later became current is readily understandable. It was a useful ideology for a group anxious to assert the novelty of their approach, a novelty which they in fact felt quite keenly.But if the primary effect of the zymase controversy was on those predisposed to accept zymase, then obviously the success of zymase depended on the fact that change had already begun to occur. Indeed, one of the most striking, and again unexpected, results of this study is the extent to which the importance of enzymes was already recognized in the early 1890's. The new immunology clearly pointed the way. Macfadyen and Hans Buchner were looking for active proteins inside the cell in 1893. Reynolds Green, Wroblewski, and Pfeffer had all anticipated the discovery of a fermentation enzyme. Other discoveries in enzymology in the 1890's pointed the same way.114 Moreover, it is clear from this study that the old protoplams theory was adapting to the new discoveries concerning the importance of enzymes. The sidechains of the old protoplasm molecule were simply reinterpreted as enzymes, as in Wroblewski's theory, for example, or in Paul Ehrlich's extremely influential “sidechain theory” of antibody formation (1897). Despite the later views of Hopkins et al., the old protoplasm and the new enzyme theories were not irreconcilable; a continuity of development had already begun when zymase came so dramatically on the scene. Buchner himself observed that the difference between the two views had become largely verbal; in retrospect we might say, not verbal, but social and historical. The gap between the continuous change in ideas and the contemporary feeling of sharply discontnuous change is a measure of the elusive but real social and historical implications of the zymase debate, of the demise of an old establishment, and the emergence of a new.In retrospect, then, it is clear that a trend was already under way in various quarters when zymase appeared. But it was still a collection of isolated and dispersed events. The zymase controversy made the trend visible and gave it a dramatic unity. The debate influenced those who had already begun to change. It was so effective because things had begun to change and because it coincided with the direction of that trend. (shrink)

In lieu of an abstract, here is a brief excerpt of the content:Kennedy Institute of Ethics Journal 14.1 (2004) 47-54 [Access article in PDF] Ethical Guidelines for Human Embryonic Stem Cell Research*(A Recommended Manuscript) Adopted on 16 October 2001Revised on 20 August 2002 Ethics Committee of the Chinese National Human Genome Center at Shanghai, Shanghai 201203 Human embryonic stem cell (ES) research is a great project in the frontier of biomedical science for the twenty-first century. Be- cause the (...) research involves the use of human embryos, it triggers serious debate on ethical issues. Opponents consider the embryo to be an early form of human life that should be respected and not destroyed. However, the majority of scientists support embryonic stem cell research, believing that it offers good prospects for the treatment of diseases that have remained incurable until now and so will benefit humankind. The Ethics Committee of the Department of Ethical, Legal, and Social Implications of the Chinese National Human Genome Center at Shanghai seriously discussed the ethical debate initiated by embryonic stem cell research. We concluded that we should support the scientists of our country in actively carrying out human embryonic stem cell research for the noble cause of "medicine being a beneficent art." For the healthy and orderly development of human embryonic stem cell research in our country, we put forward the following recommended Ethical Guidelines for Human Embryonic Stem Cell Research as a reference for leaders, administrative departments, and related scientists. Preface Article 1. Human embryonic stem cells are the primitive cells that play the main role in the growth and development of a human body. These [End Page 47] primitive cells have the potential for infinite proliferation, self-renewal, and multi-directional differentiation. If scientists can discover the mechanism of differentiation of human embryonic stem cells, it will be possible to induce differentiation of human embryonic stem cells to form various types of human cells for clinical cell therapy. If human embryonic stem cell research can be integrated with modern biomedical engineering techniques, it also will be possible to make repair and replacement of human tissues and organs a reality. Article 2. There are two ways to classify human embryonic stem cells. One way is to classify them according to their potential for differentiation. There could be three kinds of stem cells: totipotent stem cells, pluripotent stem cells, and unipotent stem cells.A totipotent stem cell has the potential to develop into a whole individual. It can differentiate into the more than 200 cell types in the whole body, construct any tissue or organ of the body, and finally develop into a whole individual. The fertilized egg and the cleavage cells at the very early stage of embryonic development are totipotent stem cells.A pluripotent stem cell has the potential to differentiate into many cell types derived from the three embryonic layers. However, it has lost the capacity to develop into a complete organism.A unipotent stem cell is derived from the further differentiation of the pluripotent stem cell. It can differentiate only into one cell type such as a hematopoietic stem cell, neural stem cell, and others.The other way is to classify human stem cells according to their source. There could be two kinds of human stem cells: embryonic stem cells and tissue stem cells (also called adult stem cells). The former involves experimentation with embryos, which has serious ethical implications. Ethical issues associated with the latter are mainly expressed in the various opinions regarding the allocation of health resources. Article 3. Human embryonic stem cells are the group of cells called the blastocyst inner cell mass during the early stage of embryonic development. They are the main source of totipotent stem cells, and hence the focal and hot point in stem cell research. Studies on the clinical application of embryonic stem cells probably will involve use of the somatic cell nucleus transfer (SCNT) technique, which destroys the early human embryo. At present, the ethical and moral debate is very serious in human embryonic stem cell research regarding whether the research will develop... (shrink)

Ecological Psychology and Enactivism both challenge representationist cognitive science, but the two approaches have only begun to engage in dialogue. Further conceptual clarification is required in which differences are as important as common ground. This paper enters the dialogue by focusing on important differences. After a brief account of the parallel histories of Ecological Psychology and Enactivism, we cover incompatibility between them regarding their theories of sensation and perception. First, we show how and why in ecological theory perception is, crucially, (...) not based on sensation. We elucidate this idea by examining the biological roots of work in the two fields, concentrating on Gibson and Varela and Maturana. We expound an ecological critique of any sensation-based approach to perception by detailing two topics: classic retinal image theories and perception in single-celled organisms. The second main point emphasizes the importance of the idea of organism-environment mutuality and its difference from structural coupling of sensations and motor behavior. We point out how ecological - phenomenological methods of inquiry grow out of mutualism and compare Gibson’s idea of visual kinesthesis to Merleau-Ponty’s idea of the lived body. Third, we conclude that Ecological Psychology and varieties of Enactivism are laying down different paths to pursue related goals. Thus, convergence of Ecological Psychology and Enactivism is not possible given their conflicting assumptions, but cross-fertilization is possible and desirable. (shrink)

This article addresses some crucial assumptions that are rarely acknowledged when organisms and machines are compared. We begin by presenting a short historical reconstruction of the concept of “machine.” We show that there has never been a unique and widely accepted definition of “machine” and that the extant definitions are based on specific technologies. Then we argue that, despite the concept's ambiguity, we can still defend a more robust, specific, and useful notion of machine analogy that accounts for successful strategies (...) in connecting specific devices (or mechanisms) with particular living phenomena. For that purpose, we distinguish between what we call “generic identity” and proper “machine analogy.” We suggest that “generic identity”—which, roughly stated, presumes that some sort of vague similarity might exist between organisms and machines—is a source of the confusion haunting many persistent disagreements and that, accordingly, it should be dismissed. Instead, we endorse a particular form of “machine analogy” where the relation between organic phenomena and mechanical devices is not generic but specific and grounded on the identification of shared “invariants.” We propose that the machine analogy is a kind of analogy as proportion and we elucidate how this is used or might be used in scientific practices. We finally argue that while organisms are not machines in a generic sense, they might share many robust “invariants,” which justify the scientists' use of machine analogies for grasping living phenomena. (shrink)

Among emotions, surprise has been extensively studied in psychology. In linguistics, surprise, like other emotions, has mainly been studied through the syntactic patterns involving surprise lexemes. However, little has been done so far to correlate the reaction of surprise investigated in psychological approaches and the effects of surprise on language. This cross-disciplinary volume aims to bridge the gap between emotion, cognition and language by bringing together nine contributions on surprise from different backgrounds - psychology, human-agent interaction, linguistics. Using different methods (...) at different levels of analysis, all contributors concur in defining surprise as a cognitive operation and as a component of emotion rather than as a pure emotion. Surprise results from expectations not being met and is therefore related to epistemicity. Linguistically, there does not exist an unequivocal marker of surprise. Surprise may be either described by surprise lexemes, which are often associated with figurative language, or it may be expressed by grammatical and syntactic constructions. Originally published as a special issue of Review of Cognitive Linguistics 13:2 (2015). (shrink)

Is it permissible to use a human embryo in stem cell research, or in general as a means for benefit of others? Acknowledging each embryo as an object of moral concern, Louis M.Guenin argues that it is morally permissible to decline intrauterine transfer of an embryo formed outside the body, and that from this permission and the duty of beneficence, there follows a consensus justification for using donated embryos in service of humanitarian ends. He then proceeds to show how (...) this justification commands assent even within moral and religious views commonly thought to oppose embryo use. Beneath his moral reasoning lies a carefully constructed metaphysical foundation incorporating accounts of the ontology of development, embryos, and species. He also incisively discusses nonreprocloning, reprocloning, ectogenesis, and related scientific frontiers. This compelling philosophical study will interest all concerned to understand virtue and obligation in the relief of suffering. (shrink)

What are cells? How are they related to each other and to the organism as a whole? These questions have exercised biology since Schleiden and Schwann (1838–1839) first proposed cells as the key units of structure and function of all living things. But how do we try to understand them? Through new technologies like the achromatic microscope and the electron microscope. But just as importantly, through the metaphors our culture has made available to biologists in different periods and places. (...) These two new volumes provide interesting history and philosophy of the development of cell biology. Reynolds surveys the field's changing conceptual structure by examining the varied panoply of changing metaphors used to conceptualize and explain cells – from cells as empty boxes, as building blocks, to individual organisms, to chemical factories, and through many succeeding metaphors up to one with great currency today: cells as social creatures in communication with others in their community. There is some of this approach in theVisionsedited collection as well. But this collection also includes rich material on the technologies used to visualize cells and their dialectical relationship with the epistemology of the emerging distinct discipline of cell biology. This volume centres on, but is not limited to, ‘reflections inspired by [E.V.] Cowdry's [1924 volume]General Cytology’; it benefits from a conference on the Cowdry volume as well as a 2011 Marine Biological Lab/Arizona State University workshop on the history of cell biology. (shrink)

Nurses and midwives are part of health care in all the stages of our lives from preconception to death. Recent scientific advances have introduced new techniques of screening and diagnosis linked to stem cell isolation and therapies. These could affect us at any age and therefore nurses will be involved as carers and patients advocates for these techniques. In this article stem cell techniques and therapies are outlined, as well as some of the ethical challenges faced by various (...) nursing groups, whether in adult, learning difficulties, mental health, paediatric, primary care, public health or health visiting areas. Nurses have to understand the ethical issues and the rights of all parties (donor, recipient and families), which may conflict with each other, to be able to weigh up the benefits and costs to each group involved. Answers have to be found on a case-by-case basis within local moral frameworks and law. Nurses represent all parties in these therapies and act as advocates for every patient group. They need to act in an interprofessional environment to promote the best interests of all their clients, both clinically and ethically. (shrink)

This article explores the development of a novel biomedical research organism, and its potential to remake the species and spaces of translational medicine. The humanized mouse is a complex experimental object in which mice, rendered immunodeficient through genetic alteration, are engrafted with human stem cells in the hope of reconstituting a human immune system for biomedical research and drug testing. These chimeric organisms have yet to garner the same commentary from social scientists as other human–animal hybrid forms. Yet, they (...) are rapidly being positioned as central to translational medicine in immunological research and pharmaceutical development. This article explores the complex relations between species and spaces they seek to enact. Humanizing mice simultaneously moves these animal forms towards the intimate geographies of corporeal equivalence with humans and the expansive geographies of translational research. These multiple trajectories are achieved by the way humanized mice function as both uncertain ‘epistemic things’ and as expansive ‘collaborative things’, articulating mouse genetics with other research, notably stem cell science. In the context of post-genomics, their indeterminacy is critical to their collaborative value; their expansive potential follows as much from their biological openness as from specific expectations. Yet, these new research organisms have both accumulative and disruptive capacities, for there are patterns of interference between these trajectories, remaking boundaries between experimental practices and clinical contexts. (shrink)

“The Role of the Individual in Evolution” is a prescient yet neglected 1941 work by the 20th century’s most important paleontologist, George Gaylord Simpson. In a curious intermingling of explanation and critique, Simpson engages questions that would become increasingly fundamental in modern biological theory and philosophy. Did individuality, adaptation, and evolutionary causation reside at more than one level: the cell, the organism, the genetically coherent reproductive group, the social group, or some combination thereof? What was an individual, anyway? (...) In this introduction, we highlight two points in a wider historical context. First, recognizing the political context of Simpson’s writing profoundly deepens our understanding of the development of his science as the Modern Evolutionary Synthesis infused biology. Second, this story illuminates the emergence of debates around what would eventually come to be called multilevel selection theory. The organism-centered concept of biological individuality defended by Simpson is situated in relation to the then-emerging Synthesis, in which he was a renowned player, and also in relation to the views he opposed: the “metaphysical” ideas of paleontologists such as Henry Fairfield Osborn, who claimed that some evolutionary trends derived from potentialities already implanted in the germplasm; and the organicist ideas of Ralph W. Gerard and the Chicago School of ecologists, which he derided as all too congenial to totalitarianism. We find parallels between the ways that Simpson thought then about human individuality under totalitarianism and the way he thought about individuality in evolution; not that any causal relationship linked the two, but that commonalities of hierarchical structure exist between single entities and groups in both instances. We then trace the subsequent development of Simpson’s political and philosophical takes on the role of the individual in evolution through the 1960s and lightly sketch out the later fate of the organicist ideas of the Chicago School. Simpson’s paper, originally published in the Journal of the Washington Academy of Sciences, is available as supplementary material in the online version of this article, as part of the "Classics in Biological Theory" collection. (shrink)

Constructivist biosemiotics foundations imply the first-person basis of cognition. CBF are developed by the biology of cognition, relational biology, enactive approach, ecology of mind, second order cybernetics, genetic epistemology, gestalt, ecological perception and affordances, and active inference by minimization of free energy. CBF reject the idea of an objective independent reality to be represented by information processing in order to be the fittest. CBF assumes that perception is the behavioral configuration of an object and objects are tokens for eigen-behaviors. Cognition (...) takes place in the organism-environment structural coupling during the ontogeny and phylogeny of all biological unities including unicellular organisms. Therefore, if exogenous DNA particles are just tokens for the cell signalling eigen-behaviors, if there is no ‘information’ in the DNA sequence, how can we explain that the same virus or trans- sequence is associated with a similar phenotype? We call this ‘exogenomic problem’. With this basic example, but sufficiently generic to the whole biological world, we agree respectively with Autopoiesis, -system, and Gaia theory: i) ‘Information, code and meaning’ in the DNA sequence belong to the domain of the observer’s description. ii) Genetic ‘information’ is not a program or algorithmic software in DNA sequence. Rather it is a microphysical observable mode of eigen-behaviors in biological unities. iii) The transfer and acquisition of DNA particles is a biospheric phenomenon that maintains its homeorhesis, symbiotic and biosemiotic entailment. Based on the theoretical and experimental results of these theories, it is concluded that genetic ‘information’ is not a genomic sequence, nor any kind of information, but for the cell DNA must embody physical forcing. Genetic characters are the effects and not the cause of phenotype and DNA particles do not ‘use or manipulate’ cellular metabolism. Rather, any cellular configuration change that occurred before or during DNA perturbation is determined on the basis of the cellular standpoint. (shrink)

This book presents the framework for a new, comprehensive approach to cognitive science. The proposed paradigm, enaction, offers an alternative to cognitive science's classical, first-generation Computational Theory of Mind. _Enaction_, first articulated by Varela, Thompson, and Rosch in _The Embodied Mind_, breaks from CTM's formalisms of information processing and symbolic representations to view cognition as grounded in the sensorimotor dynamics of the interactions between a living organism and its environment. A living organism enacts the world it lives in; (...) its embodied action in the world constitutes its perception and thereby grounds its cognition. _Enaction_ offers a range of perspectives on this exciting new approach to embodied cognitive science. Some chapters offer manifestos for the enaction paradigm; others address specific areas of research, including artificial intelligence, developmental psychology, neuroscience, language, phenomenology, and culture and cognition. Three themes emerge as testimony to the originality and specificity of enaction as a paradigm: the relation between first-person lived experience and third-person natural science; the ambition to provide an encompassing framework applicable at levels from the cell to society; and the difficulties of reflexivity. Taken together, the chapters offer nothing less than the framework for a far-reaching renewal of cognitive science. Contributors: Renaud Barbaras, Didier Bottineau, Giovanna Colombetti, Diego Cosmelli, Hanne De Jaegher, Ezequiel A. Di Paolo. Andreas K. Engel, Olivier Gapenne, Véronique Havelange, Edwin Hutchins, Michel Le Van Quyen, Rafael E. Núñez, Marieke Rohde, Benny Shanon, Maxine Sheets-Johnstone, Adam Sheya, Linda B. Smith, John Stewart, Evan Thompson. (shrink)

John Dupré explores recent revolutionary developments in biology and considers their relevance for our understanding of human nature and human society. Epigenetics and related areas of molecular biology have eroded the exceptional status of the gene and presented the genome as fully interactive with the rest of the cell. Developmental systems theory provides a space for a vision of evolution that takes full account of the fundamental importance of developmental processes. Dupré shows the importance of microbiology for a proper (...) understanding of the living world, and reveals how it subverts such basic biological assumptions as the organisation of biological kinds on a branching tree of life, and the simple traditional conception of the biological organism. (shrink)

Metagenomics is an emerging microbial systems science that is based on the large-scale analysis of the DNA of microbial communities in their natural environments. Studies of metagenomes are revealing the vast scope of biodiversity in a wide range of environments, as well as new functional capacities of individual cells and communities, and the complex evolutionary relationships between them. Our examination of this science focuses on the ontological implications of these studies of metagenomes and metaorganisms, and what they mean for common (...) sense and philosophical understandings of multicellularity, individuality and organism. We show how metagenomics requires us to think in different ways about what human beings are and what their relation to the microbial world is. Metagenomics could also transform the way in which evolutionary processes are understood, with the most basic relationship between cells from both similar and different organisms being far more cooperative and less antagonistic than is widely assumed. In addition to raising fundamental questions about biological ontology, metagenomics generates possibilities for powerful technologies addressed to issues of climate, health and conservation. We conclude with reflections about process-oriented versus entity-oriented analysis in light of current trends towards systems approaches. (shrink)

When I read this paragraph about her book: -/- In Form, Matter, Substance, Kathrin Koslicki develops a contemporary defence of the Aristotelian doctrine of hylomorphism. According to this approach, objects are compounds of matter (hule) and form (morphe or eidos) and a living organism is not exhausted by the body, cells, organs, tissue, and the like that compose it. Koslicki argues that a hylomorphic analysis of concrete particular objects is well equipped to compete with alternative approaches when measured against (...) a wide range of criteria of success. However, a plausible application of the doctrine of hylomorphism to the special case of concrete particular objects hinges on how hylomorphists conceive of the matter composing a concrete particular object, its form, and the hylomorphic relations which hold between a matter-form compound, its matter and its form. Koslicki offers detailed answers to the questions surrounding this approach to the metaphysics of concrete particular objects. As a result, matter-form compounds emerge as occupying the privileged ontological status traditionally associated with substances, despite their metaphysical complexity, due to their high degree of unity. (shrink)

The concept of information has acquired a strikingly prominent role in contemporary biology. This trend is especially marked within genetics, but it has also become important in other areas, such as evolutionary theory and developmental biology, particularly where these fields border on genetics. The most distinctive biological role for informational concepts, and the one that has generated the most discussion, is in the description of the relations between genes and the various structures and processes that genes play a role in (...) causing. For many biologists, the causal role of genes should be understood in terms of their carrying information about their various products. That information might require the cooperation of various environmental factors before it can be "expressed," but the same can be said of other kinds of message. An initial response might be to think that this mode of description is entirely anchored in a set of well-established facts about the role of DNA and RNA within protein synthesis, summarized in the familiar chart representing the "genetic code," mapping DNA base triplets to amino acids. However, informational enthusiasm in biology predates even a rudimentary understanding of these mechanisms (Schrodinger 1944). And more importantly, current applications of informational concepts extend far beyond anything that can receive an obvious justification in terms of the familiar facts about the specification of protein molecules by DNA. This includes: 1 (i) The description of whole-organism phenotypic traits (including complex behavioral traits) as specified or coded for by information contained in the genes, (ii) The treatment of many causal processes within cells, and perhaps of the wholeorganism developmental sequence, in terms of the execution of a program stored in the genes, (iii) The idea that genes themselves, for the purpose of evolutionary theorizing, should be seen as, in some sense, "made" of information.. (shrink)

Drawing on models of communication due to Lewis and Skyrms, I contrast sender-receiver systems as they appear within and between organisms, and as they function in the bridging of space and time. Within the organism, memory can be seen as the sending of messages over time, communication between stages as opposed to spatial parts. Psychological memory and genetic memory are compared with respect to their relations to a sender-receiver model. Some puzzles about “genetic information” can be resolved by seeing (...) the genome as a cell-level memory with no sender. (shrink)

Understanding how transcription factor (TF) binding is related to gene regulation is a moving target. We recently uncovered genome‐wide evidence for a “Hit‐and‐Run” model of transcription. In this model, a master TF “hits” a target promoter to initiate a rapid response to a signal. As the “hit” is transient, the model invokes recruitment of partner TFs to sustain transcription over time. Following the “run”, the master TF “hits” other targets to propagate the response genome‐wide. As such, a TF may act (...) as a “catalyst” to mount a broad and acute response in cells that first sense the signal, while the recruited TF partners promote long‐term adaptive behavior in the whole organism. This “Hit‐and‐Run” model likely has broad relevance, as TF perturbation studies across eukaryotes show small overlaps between TF‐regulated and TF‐bound genes, implicating transient TF‐target binding. Here, we explore this “Hit‐and‐Run” model to suggest molecular mechanisms and its biological relevance. (shrink)

In recent years, the publication of the studies on the transmissibility in mammals of the H5N1 influenza virus and synthetic genomes has triggered heated and concerned debate within the community of scientists on biological dual-use research; these papers have raised the awareness that, in some cases, fundamental research could be directed to harmful experiments, with the purpose of developing a weapon that could be used by a bioterrorist. Here is presented an overview regarding the dual-use concept and its related international (...) agreements which underlines the work of the Australia Group Export Control Regime. It is hoped that the principles and activities of the AG, that focuses on export control of chemical and biological dual-use materials, will spread and become well known to academic researchers in different countries, as they exchange biological materials and scientific papers. To this extent, and with the aim of drawing the attention of the scientific community that works with yeast to the so called Dual-Use Research of Concern, this article reports case studies on biological dual-use research and discusses a synthetic biology applied to the yeast Saccharomyces cerevisiae, namely the construction of the first eukaryotic synthetic chromosome of yeast and the use of yeast cells as a factory to produce opiates. Since this organism is considered harmless and is not included in any list of biological agents, yeast researchers should take simple actions in the future to avoid the sharing of strains and advanced technology with suspicious individuals. (shrink)

Abstract“Sign stimuli” elicit specific patterns of behavior when an organism's motivation is appropriate. In the toad, visually released prey-catching involves orienting toward the prey, approaching, fixating, and snapping. For these action patterns to be selected and released, the prey must be recognized and localized in space. Toads discriminate prey from nonprey by certain spatiotemporal stimulus features. The stimulus-response relations are mediated by innate releasing mechanisms (RMs) with recognition properties partly modifiable by experience. Striato-pretecto-tectal connectivity determines the RM's recognition and (...) localization properties, whereas medialpallio-thalamo-tectal circuitry makes the system sensitive to changes in internal state and to prior history of exposure to stimuli. RMs encode the diverse stimulus conditions referring to the same prey object through different combinations of “specialized” tectal neurons, involving cells selectively tuned to prey features. The prey-selective neurons express the outcome of information processing in functional units consisting of interconnected cells. Excitatory and inhibitory interactions among feature-sensitive tectal and pretectal neurons specify the perceptual operations involved in distinguishing the prey from its background, selecting its features, and discriminating it from predators. Other connections indicate stimulus location. The results of these analyses are transmitted by specialized neurons projecting from the tectum to bulbar/spinal motor systems, providing a sensorimotor interface. Specific combinations of such projective neurons – mediating feature- and space-related messages – form “command releasing systems” that activate corresponding motor pattern generators for appropriate prey-catching action patterns. (shrink)

Like most bilaterian animals, the annelid Platynereis dumerilii generates the majority of its body axis in an anterior to posterior temporal progression with new segments added sequentially. This process relies on a posterior subterminal proliferative body region, known as the "segment addition zone" (SAZ). We explored some of the molecular and cellular aspects of posterior elongation in Platynereis, in particular to test the hypothesis that the SAZ contains a specific set of stem cells dedicated to posterior elongation.We cloned and characterized (...) the developmental expression patterns of orthologs of 17 genes known to be involved in the formation, behavior, or maintenance of stem cells in other metazoan models. These genes encode RNA-binding proteins(e.g., tudor, musashi, pumilio) or transcription factors(e.g., myc, id, runx) widely conserved in eumetazoans. Most of these genes are expressed both in the migrating primordial germ cells and in overlapping ring-like patterns in the SAZ, similar to some previously analyzed genes(piwi, vasa). The SAZ patterns are coincident with the expression of proliferation markers cyclin B and PCNA. EdU pulse and chase experiments suggest that new segments are produced through many rounds of divisions from small populations of teloblast-like posterior stem cells. The shared molecular signature between primordial germ cells and posterior stem cells in Platynereis thus corresponds to an ancestral "stemness" program. (shrink)

In lieu of an abstract, here is a brief excerpt of the content:Reviewed by:Hegel’s Theory of Self-Conscious Life by Guido SeddoneWill DesmondSEDDONE, Guido. Hegel’s Theory of Self-Conscious Life. Leiden: Brill, 2023. 155 pp. Cloth, $138.00Guido Seddone’s monograph explores an ensemble of issues centering on what he terms Hegelian “naturalism.” He argues that “Hegel’s philosophy represents a novel version of naturalism since it stresses the mutual dependence between nature and spirit, rather than just conceiving of spirit as a substance emerging and (...) separating from bodily natural requisites.” Seddone avoids scholarly exegeses to address instead “theoretical and systematic aspects of the Hegelian philosophy.” He focusses on “life” and “self-consciousness” as the conceptual keys to those parts of Hegel that remain compelling for relevant contemporary debates. “This book is, therefore, based on the dialogue between Hegel [End Page 361] and contemporary thinkers and strives to enhance our understanding of theoretical and practical issues and to widen the grammar of the philosophical thought.” The book’s chapters proceed from the more abstract to the more concrete—essentially from issues of logic, epistemology, and psychology to morality, society, and history.Chapter 1 (“Science of Logic: The Logical Premises of Hegel’s Naturalism”) argues that the categories of “Teleology” and “Life” in Hegel’s Science of Logic mark the critical transition in his naturalism from the sciences of physics (“Mechanism”) and chemistry (“Chemism”) to biology, as well as from external nature to inner self-consciousness and cognition. Seddone helpfully points to Hegel’s revisions of Kant’s subordination of teleological language (merely heuristic) to mechanical explanation. Most promising is the comparison of the “self-referring negativity” of Hegelian “life” to discussions by Evan Thompson and Francisco Varela of the cell—whose permeable membrane enables it to be more than its merely chemical environment.Chapter 2 (“Self-Consciousness”) takes a rather bird’s-eye approach to the Phenomenology of Spirit, offering a basic reading of Hegelian self-consciousness and Geist in relation to the Cartesian cogito and Kantian unity of apperception. Scattered remarks about animal desire and the master–slave relation could be clarified to better explore a naturalistic basis of the Hegelian conception of mind. One is struck by the dearth of specific texts from the section “Self-Consciousness”: Seddone seems content with some well-known quotations (for example, Geist as an “I that is We and We that is I”) punctuating large generalizations.Chapter 3 does not quite live up to its title (“The Hegelian Theory about the (Human) Biological Organism”) in that it focuses primarily on Hegel’s “treatise about habits” in the Encyclopaedia of the Philosophical Sciences. Here habit is construed as a second nature, and hence a further step toward self-conscious, relational mind: Habits are “universal ways of the soul, i.e. ways in which individual soul [sic] incorporates feelings by evolving general rules and practices.”The last section of chapter 4 (“Extended and Embodied Mind”) reverts to habits as moments of the feeling soul but dissociates Hegel’s notion of Verleiblichung from contemporary discussions of embodied mind. By contrast, Seddone argues for retranslating Hegelian Geist as “common mind” and juxtaposes this with the related concept of mind (in, for example, Philip Pettit) as “extended” through social entities, with the result that Hegel’s approach is praised as “the state-of-the-art of this topic.”Chapter 5 (“Natural and Self-conscious Agency”) is perhaps the clearest chapter as it presents the dialectic of the abstractly universal will in the initial sections of Philosophy of Right, links this and the Hegelian conception of free agency to his logical category of “actuality,” and proceeds to an illuminating contrast of the Hobbesian and Hegelian visions of society and state. [End Page 362]In tackling attempts to reconcile “Normativity and Freedom,” chapter 6 spends over six pages rehearsing the basics of Kantian autonomy before turning to Hegel’s Phenomenology of Spirit, specifically the master–slave dialectic (again) as the critical moment in the evolution of social norms. “My thesis is that self-conscious life needs recognition in order to achieve the higher form of independence created by social acknowledgement and justification, what [sic] fosters the condition for an authoritative reason that can be socially... (shrink)

Selected by Choice Magazine as an Outstanding Academic Title What is so special about human life? What is the relationship between flesh and blood and the human soul? Is there a kind of life that is worse than death? Can a person die and yet the human organism remain in some real sense alive? Can souls become sick? What justifies cutting into a living human body? These and other questions, writes neurosurgeon and philosopher Grant Gillett, pervade hospital wards, clinical (...) offices, and operating rooms. In Bioethics in the Clinic: Hippocratic Reflections, Gillett brings the tools of philosophy to bear on some of the most pressing issues confronting bioethicists today. Gillett draws on many schools of thought, including analytic, moral, and postmodern philosophy; utilitarianism; classical ethical theory; phenomenology; and metaphysics. He engages the reasoning of such philosophers as Aristotle, Nietzsche, Wittgenstein, Foucault, Habermas, Levinas, and Martha Nussbaum, and offers both practical and clinical insights into such topics as the principle of "Do no harm," informed consent, confidentiality, cloning, and euthanasia. Opening with an explanation of the axioms to be traced throughout succeeding discussions, with special emphasis on Hippocratic principles, Gillett focuses on general and specific problems of clinical practice, particularly as they affect the physician-patient relationship. The author then goes on to address ethical problems related to both the end of life, including euthanasia, and the beginning of life, such as embryo and stem cell research. Rigorous and elegant, this book will be of interest to those in medical fields, to students and scholars of philosophy, and to lay readers interested in the profound ethical dramas played out in hospitals and doctors' offices every day. (shrink)

Only those whose work and interests have led them to notice it, will have realised, in all probability, the remarkable extent to which the term organization has gained currency, or acquired new and special emphasis, throughout the entire range of scientific and sociological literature during the last ten or twenty years.In biology and bio-chemistry organization has been discussed or used as a technical term, mostly since 1930 by at least thirty well-known authors; amongst the more prominent are Huxley, Wilson, Woodger, (...) Cannon, Waddington, McDougall, Needham, Block, Hopkins and Sherrington. Under this magic term some authors refer to the physico-chemical nature of the cell or cytoplasm, and usually with special reference to selective or directive catalysis; others to the general constitution or structure of the organism and almost indistinguishable from general morphology and physiology; others to embryological development as such ; others more especially to “relations” between cells, organs and structural parts, often in an abstract sense; others refer more particularly to a hypothetical integrating and/or co-ordinating factor : a few refer to re-constitution from dissociated cells as observed in experiments with Sponges and Hydroids. (shrink)

Michael Nair-Collins and Franklin Miller are right to emphasise that, in order to deliberate responsibly about ethical and legal questions related to brain death and organ donation, it is crucial to answer the question of whether or not ‘brain death’i does indeed mark the biological death of the organism. Nonetheless, I disagree with the authors’ conclusion that brain death does not indicate the death of the human organism. Death can never be defined in merely biological terms, because any (...) biological conception of death relies on metaphysical presuppositions regarding what it means to be an ‘organism as a whole’, rather than an aggregate of cells and tissues. Death is a change in substance —that is, a change from one type of entity to another — not the cessation of all biological life. Organismal death occurs well before all of the organism’s parts irreversibly cease vital activity and decompose into inorganic matter. Biological life in some form can and usually does continue after organismal death at least for a time, with recent evidence indicating that animal cell networks continue to perform complex functions like stress response, immune response and inflammation response up to several days postmortem.1 With external support, many cells and tissues can continue to perform their functions ex vivo for long periods of time or even indefinitely.2 Henrietta Lax died in 1951, but cells derived from her cancerous cervical cells …. (shrink)

Life as a complicated process is composed of causal phenomena. But even if we know the reasons of all that happens in a living organism, we do not know what life really is. The problem of intercausal relation, of “causal structure” remains. The reason why a process takes place, must be found by analysis, causal structures are found by synthesis of the results of this analysis. Causal structures are characterized by two kinds of equilibrium: energetic and specific equilibrium. (...) A state of physical equilibrium is characterized by a minimum of free energy; a biological energetic equilibrium is an organized one, where the vital factors activate the production of energy by each other and force each other to limit that production to the necessary measure. A specific equilibrium is characterized by the properties of its factors, properties by which those factors act as a cause after having received a specific stimulation. Every factor possesses two specific properties, in accordance with the properties of two neighbouring factors, as a link between two other links in a chain . Both forms of equilibrium authorise us to speak of living systems as a “whole”. In the second part of this paper we treat the dynamic aspect of the functions of living systems as a “whole”. This dynamic aspect manifests itself in growth and probably in cortical functions. Blastomeres represent, when isolated, the “whole” of growing potentialities of a germe. In normal contact with each other they restrict themselves to produce a part of that “whole”, in harmony with that which other blastomeres produce. This harmonious restriction can be explained by interaction between all the blastomeres by which every blastomere suppresses in other blastomeres all that it will produce itself. Blastomeres must therefore act on other blastomees not according to their isolate “being”, but according to the influences which they undergo by all other blastomeres, that means according to their “rôle”. There must be a causal net of interaction between all the blastomeres and that net “as a whole” determines every step of growth. Such a net of relation determines also human history and sociology. Materialism only took account of isolated causes, vitalism only of the effect of the net of causal relations without understanding that such a net might be analysed. In reality there is neither materialism nor vitalism.La vie est un phénomène complexe, se composant de différents phénomènes causals, qui un jour peut-être seront réduits à la causalité physique et chimique. Cependant connaitre toutes les causes des phénomènes vitaux ne signifie pas connaître la vie. Le problème de la vie ne se borne pas aux rapports causals, mais implique surtout les rapports intercausals, c'est à dire l'harmonie ou l'équilibre de ses parties constituantes. La vie comme phénomène est provoquée par une „structure causale”. Tandis que les causes sont trouvées par l'analyse, les rapports intercausals doivent être recherchés par la synthèse, c'est-à-dire par la réconstruction de la réalité de l'organisme vivant en se servant des données analytiques. Le système vivant est en équilibre énergétique et spécifique. Les facteurs énergétiques sont interlacés de telle façon, qu'ils s'activent entre eux et qu'ils se forcent entre eux à se resteindre au développement de l'énergie nécessaire. Un équilibre physique c'est l'état d'énergie libre minimum, tandis que l'équilibre biologique c'est un état d'énergie organisée. Dans un équilibre spécifique on ne peut se borner aux effects causals se manifestant par un phénomène. Il faut décrire les rapports des propriétés spécifiques de tous les facteurs; ce sont ces propriétés qui leur permettent d'agir comme cause, lorsqu'-ils sont atteint d'une excitation spécifique. Les facteurs possèdent au moins deux propriétés spécifiques, adaptées à deux facteurs voisins, comme chaque anneau d'une chaine s'adaptant à deux anneaux voisins . Le fait que l'on trouve dans chaque individu ces deux formes d'équilibre nous donne le droit de créer le concept du „tout” par rapport auquel on peut constater l'harmonie de tous les tacteurs.C'est là le „tout statique”, reste encore le „tout dynamique” qui se manifeste par la croissance et probablement par les phénomènes se produisant dans l'écorce cérébrale, base des actes psychiques. Les parties représentent beaucoup de possibilités qui ne se réalisent pas; p.e. les blastomères peuvent représenter le „tout” de l'organisme, tandis qu'ils se borneront dans la croissance normale à la production d'une part de l'individu. Il y a une interaction entre tous les blastomères, de façon que, par la suppression ou par l'activation mutuelle, chaque partie réalise ce que lui laissent les autres et ce qui est en harmonie avec ce que produiront les autres. De cette façon il y aura de l'harmonie dans tout ce qui sera produit. Les parties agissent par cette interaction, non selon leur „être”, en tant que cellule isolée, mais selon leur „rôle” dans le „tout” du germe, rôle qui est déterminé par cette interaction mutuelle universelle. C'est cette interaction qui détermine le „patron causal”, responsable de chaque étappe de la coissance. Ainsi ce ne sont pas les facteus isolés, mais le réseau des rapports établis entre tous les facteurs, qui gouvernent les phénomènes de la croissance. Ce réseau, par activation ou par suppression, détermine à chaque instant les propriétés causales des parties, d'entre toutes les multiples possibilités. Les possibilités étant données dans les cellules, c'est le „tout” du réseau des rapports qui détermine la croissance. Le matérialisme n'a vu que les causes isolées, telles qu'ellés se manifestent dans les expériences des physiciens, grâce à la technique; le vitalisme n'a vu que le „tout”, sans tâcher de l'analyser afin de trouver à sa base le système causal compliqué, que nous avons tâché de décrire. Dans la réalité la théorie du causalisme ni celle du vitalisme le tiennent plus de bout. (shrink)

Apoptosis proteins have a central role in the development and homeostasis of an organism. These proteins are very important for understanding the mechanism of programmed cell death, and their function is related to their types. According to the classification scheme by Zhou and Doctor (2003), the apoptosis proteins are categorized into the following four types: (1) cytoplasmic protein; (2) plasma membrane-bound protein; (3) mitochondrial inner and outer proteins; (4) other proteins. A powerful learning machine, the Support Vector Machine, (...) is applied for predicting the type of a given apoptosis protein by incorporating the sqrt-amino acid composition effect. High success rates were obtained by the re-substitute test (98/98 = 100 %) and the jackknife test (89/98 = 90.8%). (shrink)

In recent years we have seen a dramatic shift, in several different areas of communication studies, from an information-theoretic to a dynamic systems paradigm. In an information processing system, communication, whether between cells, mammals, apes, or humans, is said to occur when one organism encodes information into a signal that is transmitted to another organism that decodes the signal. In a dynamic system, all of the elements are continuously interacting with and changing in respect to one another, and (...) an aggregate pattern emerges from this mutual co-action. Whereas the information-processing paradigm looks at communication as a linear, binary sequence of events, the dynamic systems paradigm looks at the relation between behaviors and how the whole configuration changes over time. One of the most dramatic examples of the significance of shifting from an information processing to a dynamic systems paradigm can be found in the debate over the interpretation of recent advances in ape language research (ALR). To some extent, many of the early ALR studies reinforced the stereotype that animal communication is functional and stimulus bound, precisely because they were based on an information-processing paradigm that promoted a static model of communicative development. But Savage-Rumbaugh's recent results with bonobos has introduced an entirely new dimension into this debate. Shifting the terms of the discussion from an information-processing to a dynamic systems paradigm not only highlights the striking differences between Savage-Rumbaugh's research and earlier ALR studies, but further, it sheds illuminating light on the factors that underpin the development of communication skills in great apes and humans, and the relationship between communicative development and the development of language. Key Words: apes; ape language research (ALR); brain development; co-regulation; communication; dynamic systems; language development; symbols. (shrink)

The study of a collection of metabolites as a whole (metabolome), as opposed to isolated small molecules, is a fast‐growing field promising to take us one step further towards understanding cell biology, and relating the genetic capabilities of an organism to its observed phenotype. The new sciences of metabolomics and metabonomics can exploit a variety of existing experimental and computational methods, but they also require new technology that can deal with both the amount and the diversity of the (...) data relating to the rich world of metabolites. More specifically, the collaboration between bioinformaticians and chemoinformaticians promises to advance our view of cognate molecules, by shedding light on their atomic structure and properties. Modelling of the interactions of metabolites with other entities in the cell, and eventually complete modelling of reaction pathways will be essential for analysis of the experimental data, and prediction of an organism's response to environmental challenges. BioEssays 28: 534–545, 2006. © 2006 Wiley Periodicals, Inc. (shrink)

The relationship between brain and mind has been extensively explored through the developments within neuroscience over the last decade. However, the ontological status of mind has remained fairly problematic due to the inability to explain all features of the mind through the brain. This inability has been considered largely due to partial knowledge of the brain. It is claimed that once we gain complete knowledge of the brain, all features of the mind would be explained adequately. However, a challenge to (...) such a position is downward causation: How do we explain the causal power that mental states exert over brain activities? If we agree that downward causation occurs, then to what extent could a sole explanation of brain activities account for our behaviour? (For they would in themselves be conditioned by the mental states which are left unexplained). This dissertation is an attempt to understand relation between brain and mind through the concept of emergence, placed in the context of complex systems approach. This will create a space to account for the causal power of mental states. The complex systems approach says that as the complexity of a system increases, we witness the emergence of novel qualities and after a certain threshold (of complexity), the emergence of a novel structure. When the body (and correspondingly, brain) reaches a certain level of complexity, the mind emerges. The brain is a complex system from which the mind emerges. The brain, consisting of billions of neurons interacting with each other, regulates the body placed in the environment. The interaction of neurons (local interactions involving self-organization) result in dynamical brain signatures (global synergy). Such signatures are correlative to mental states. Mind is the process of a living organism embodying an intentional stance. This object could be the subject itself or another distinct from the subject. With the emergence of mind, the causal powers of brain are conditioned by the mind. Such a conditioning is evident through the causal efficacy of mental states. While the brain is minimal condition for the mind to emerge, the mind in itself is embedded (showcased/explicated/manifested) throughout the body. The mind is a process that belongs to body-as-a-whole with the novel quality of intentionality. A preliminary to understanding this relation is its metaphysical inclination. A large portion of the history of philosophy of mind has advocated a metaphysics of entities where the mind and body have been seen as two entities with distinct essences. However, such attribution of entity-ship does not take into account the processual nature of these existents (that they are essentially dependent on their environment for their existence and sustenance). Thus, the category of processual unity has been introduced which sought to account for existent as emergent wholes that move towards a stable equilibrium through self-organization. By considering existents to be processual unities, we can account for their identity as a whole-in-itself (what has been called organizational closure) and also for their processual nature. The brain is a component of the body which is a complex system and is representative of the body’s stance in the world. The brain, consisting of billions of neurons interacting with each other, regulates the body placed in the environment. The interaction of neurons (local interactions involving self-organization) result in dynamical brain signatures (global synergy). Such signatures are correlative to mental states. These mental states in turn condition the brain patterns, that allows the embodying of mental states. Thus, the three-way process of the representation of body in the world by the brain, the emergence of mental state through dynamic brain patterns and the reciprocal causal power on the brain patterns by the mental states marks embodiment. The relation between brain, body and mind can be outlined as follows: A. There are complex interactions in the brain. These interactions are representative of the body’s stance in the world and are present in form of dynamical brain signatures. B. The dynamical brain signatures lead to emergence of mind as a process. The mental state has causal power which conditions the brain. C. The brain conditioned by causal power of the mind carries out embodiment of the mind throughout the body. In the dissertation, an exposition on relation between brain and mind through complex system approach is followed by a brief on relation between body and mind. The radical embodiment approach adopts the nonlinear dynamic systems theory to understand relation of brain, body and mind. It states a shift from mapping of cognitive states onto Neural Correlates of Consciousness to their mapping through dynamic brain signatures. Every mental state is embedded throughout the body. The dissertation explores the three features of consciousness, intentionality and qualia. These have previously formed a challenge within a dualistic framework and the dissertation intends to show a direction in which they can be accounted for, within the complex systems approach and radical embodiment viewpoint. After a certain threshold of the rate of production of cell assemblies is bypassed, we become conscious of the representation itself. This leads to emergence of phenomenal states. Qualia is the qualitative character of such states, which belong to the body-as-a-whole and for this reason, cannot be reduced to properties of any of the components from which it emerges (the dynamic brain signatures) or in which it is embodied (the body and its individual parts) alone. Intentionality is the novel property of mind of moving towards a certain set of attractors where attractors refer to the states that the system prefers (which would positively contribute to its fitness). The scope of this dissertation is to delineate the relation of brain to the mind and unravel some persistent troubles of philosophy of mind within such delineation. The types of components and their relation within the mind preceded by a thorough study of how the mind is embodied is an area yet to be extensively explored in the coming works. (shrink)

We are mastering engineering behaviour on a molecular level. A growing number of researches investigating the relationship between microbiota, human brain and behaviour examine the impacts of manipulating specific microbial colonies in human hosts. To enable discussing and understanding communicational phenomena that occur in scales not visible to the naked eye, we propose the term Molmedia – a metaphorical reference to the concept of mole, denoting here not exclusively the quantitative amount of substance but the information exchange processes (taking the (...) substances as messages) that are going on at elementary entities level such as atomic, subatomic and molecular, within a given system that can be a living organism. We take media (plural of medium) as an intervening agency, means or instrument. Interacting emitters and receivers in this system are the microbiota and the organism actual cells. Within this self-organizing structure, the ongoing informational processes produce, as an emergence, the self and behavioral patterns that can be appreciated, manipulated and cannibalized. The art and science installation Transplanting the Self: Microbiome Anthropophagy is presented as an explorative exercise of the concept and related possibilities in science concerning gut–brain communication and the use of neuroregenerative nutrition in treatments for neurologic conditions. (shrink)

The Drosophila salivary gland has emerged as an outstanding model system for the process of organ formation. Many of the component steps, from initial regional specification through cell specialization and morphogenesis, are known and many of the genes required for these different processes have been identified. The salivary gland is a relatively simple organ; the entire gland comprises of only two major cell types, which derive from a single contiguous primordium. Salivary cells cease dividing once they are specified, (...) and organ growth is achieved simply by an increase in size of individual cells, thus eliminating concerns about the potential unequal distribution of determinants during mitosis. Drosophila salivary glands form by the same cellular mechanisms as organs in higher organisms, including regulated cell shape changes, cell intercalation and directed cell migration. Thus, learning how these events are coordinated for tissue morphogenesis in an organism for which the genetic and molecular tools are unsurpassed should provide excellent paradigms for dissecting related processes in the more intricate organs of more complicated species. BioEssays 23:901–911, 2001. © 2001 John Wiley & Sons, Inc. (shrink)

Algae are significant members of Earth's biodiversity. Having been studied for a long time, the discovery of new algal phyla is extremely unusual. Recently, the enigmatic “Picobiliphyta,” a group of uncultured eukaryotes unveiled using molecular tools, were claimed to represent an unrecognized early branching algal lineage with a nucleomorph (remnant nucleus of a secondary algal endosymbiont) in their plastids. However, subsequent studies rejected the presence of a nucleomorph, and single‐cell genomic studies failed to detect any plastid‐related genes, ruling out (...) the possibility of plastid occurrence. The isolation of the first “picobiliphyte,” Picomonas judraskeda, a tiny organism that feeds on very small (<150 nm) organic particles, came as final proof of their non‐photosynthetic lifestyle. Consequently, the group has been renamed Picozoa. The passage from “picobiliphytes” to “picozoa” illustrates the crucial role that classical protistology should play to provide sound biological context for the wealth of data produced by modern molecular techniques. (shrink)

The materialist critics argue that insuperable difficulties are encountered by the hypothesis that immaterial mental events such as thinking can act in any way on material structures such as neurons of the cerebral cortex, as is diagrammed in Fig. 8. Such a presumed action is alleged to be incompatible with the conservation laws of physics, in particular of the First Law of Thermodynamics. This objection would certainly be sustained by 19th century physicists and by neuroscientists and philosophers who are still (...) ideologically in the physics of the 19th century, not recognizing the revolution wrought by quantum physicists in the 20th century. Unfortunately it is rare for a quantum physicist to dare an intrusion into the brain-mind problem. But in a recent book the quantum physicist Margenau (1984) makes a fundamental contribution. It is a remarkable transformation from 19th century physics to be told (p. 22): "that some fields, such as the probability field of quantum mechanics carry neither energy nor matter." He goes on (p. 96) to state: "In very complicated physical systems such as the brain, the neurons and sense organs, whose constituents are small enough to be governed by probabilistic quantum laws, the physical organ is always poised for a multitude of possible changes, each with a definite probability; if one change takes place that requires energy, or more or less energy than another, the intricate organism furnishes it automatically. Hence, even if the mind has anything to do with the change, that is if there is a mind-body interaction, the mind would not be called upon to furnish energy." In summary (p. 97) Margenau states that: "The mind may be regarded as a field in the accepted physical sense of the term. But it is a nonmaterial field; its closest analogue is perhaps a probability field. It cannot be compared with the simpler nonmaterial fields that require the presence of matter (e.g. gravity) nor does it necessarily have a definite position in space. And so far as present evidence goes it is not an energy field in any physical sense, nor is it required to contain energy in order to account for all known phenomena in which mind interacts with brain". In formulating more precisely the dualist hypothesis of mind-brain interaction, the initial statement is that the whole world of mental events (World 2) has an existence as autonomous as the world of matter-energy (World I ) (Fig. 1). The present interactionist hypothesis does not relate to these ontological problems, but merely to the mode of action of mental events on neural events, that is of the nature of the downward arrows across the frontier in Fig. 8. Following Margenau (1984) the hypothesis is that mind-brain interaction is analogous to a probability field of quantum mechanics, which has neither mass nor energy, yet can cause effective action at microsites. More specifically it is proposed that the mental concentration involved in intentions (Figs. 7, 8) or attention (Fig. 4) or planned thinking (Figs. 5, 6) can cause neural events by a process analogous to the probability fields of quantum mechanics. -/- We can ask: what neural events could be appropriate recipients for mental fields that are analogous to quantal probability fields? Already we may have the answer in recent discoveries on the nature of the synaptic mechanism whereby one nerve cell communicates with another. (shrink)

Resonance can trigger of a series of quantum events and therefore induce several changes related to consciousness at micro as well as macro level within a living system. Therapeutic effects have been observed in several religious meditative and healing practices, which use resonance in the form of chanting and prayers. A living system may have many resonant frequencies due to their degrees of freedom, where each can vibrate as a harmonic oscillator supporting the progression of vibrations as waves that moves (...) as a ripple within the whole system. A cell as an organism or cells in multicellular organisms act as resonating bodies that trigger of oscillation of oscillatory proteins of the cytoskeletal network. The resulting protein conformational changes generate a conscious moment that is regulated via electron tunneling, delocalization and superposition in space time geometry. Consciousness or sentience are phenomenal characteristics of every cell and even though we don’t know the “why” we surely can predict and hypothesize the “how” of consciousness to be quantum computed, which enables the cell to understand and judge perceptions giving it a prospect to behave as per will. (shrink)

In lieu of an abstract, here is a brief excerpt of the content:THE THOUGHT-EXPERIMENT: SHEWMON ON BRAIN DEATH 1 ANDREW TARDIFF University of Rhode Island Kingston, Rhode Island MODERN TECHNOLOGY as it advances often brings with it new ethical problems. One such problem is "brain death." In times past, that is, up until the 1960s, medical men considered cardiopulmonary collapse as the criterion for the death of the person, for with heart failure the body ceases to function as a whole (...) living organism. As technology and science advanced, however, scientists discovered that when the heart failed the very first organ to be irreparably damaged was the brain. Moreover, around this time they discovered how to revive the heart and to keep the body alive even after the brain had been destroyed. These discoveries and advances alone might not have sufficed to raise the issue of brain death. But science also discovered the crucial role the brain plays for consciousness and a fortiori for the specifically human abilities of knowing and willing. It is thus that we now have the question : once the brain has been irreparably damaged, and the possibility of consciousness and personal life thereby excluded, is such a person really dead, even though his body is alive and functioning? But it would be less than honest to say that this is an adequate history of the brain death criterion. For with the dawn of organ transplantation a new demand for living organs arose, one that had never been known before. Under the old cardiopulmonary criterion of death, the demand for living organs could not be met since the organs of a person " dead " in that sense of the word 1 " The Metaphysics of Brain Death, Persistent Vegetative State, and Dementia ", The Thomist, 49 (January, 1985) : 24-80. 435 436 ANDREW TARDIFF could not be transplanted; under the brain death criterion they could. Such a situation will quite naturally give rise to, or at least heavily contribute to, a less than objective handling of the issue. Happily, however, the literature on brain death has recently seen a serious objective appraisal of the issue: D. Alan Shewmon 's article The Metaphysics of Brain Death, Persistent Vegetative State, and Dementia. Shewmon argues persuasively that the new criterion of death is sound. He argues for an exact formulation of the criterion of the death of the person, viz., the death or irreparable destruction of one specific part of the brain, namely, the tertiary cortex. Thus, the death of the person occurs with the irrevocable destruction of the tertiary cortex, even if the rest of the body is still functional. In the following pages I will consider Shewmon's analysis of the issue and expose some of the major problems with his arguments. My critique will focus chiefly on an analysis of a certain thought-experiment of which Shewmon makes extensive use. I do this both because of its central role in Shewmon's argument and because of the light it sheds on the whole problem of using brain death as the criterion for the death of the person. The Thought-Experiment Shewmon has set out to show that only the teritary cortex is the critical structure or formed matter necessary for the human essence.2 In a later passage, however, he mitigates this claim slightly, in case science should someday discover that some other area (or just some fraction of this area) is the critical area.3 But in either case, Shewmon maintains that the crucial area is to be found in the neocortex of the cerebral hemespheres. By the time his analysis has reached page fifty-nine, he believes he has established this much. The following is an examination of his thoughtexperiment and how he establishes the above claim. Shewmon begins with certain observations about how the human essence relates to the various parts of the body. Modern 2 Ibid., p. 56ff. a Ibid., p. 59. SHEWMON ON BRAIN DEATH 437 technology has developed ways to remove parts of a man's body without killing either the man or the part. Science can remove a person's kidney, for example, and transplant it into another person 's body without killing either the person or destroying the living cells of the kidney. Moreover... (shrink)

The conceptual framework of this paper is the structural conception of theories as formulated by Sneed-Stegmüller. We present an informal set-theoretical axiomatization of M. F. Xavier Bichat’s theory of the constitution of the organism, which conceived the tissue as the ultimate constitutive element of the living beings, and a reformulation of our previous axiomatization of the cell theory. We propose a tentative relation of reduction between both theories which possibilitates the derivation of the axioms of the tissue (...) theory from those of the cell theory. The limits and problems of the axiomatization are discussed and brief reference is being made to some historical aspects of the reception of the cell theory. (shrink)

In lieu of an abstract, here is a brief excerpt of the content:Alzheimer's Disease, Mild Cognitive Impairment, and the Biology of Intrinsic AgingThomas B. L. Kirkwood (bio)Keywordsaging, Alzheimer’s disease, genetic mutation, mild cognitive impairment, telomereThe article by Gaines and Whitehouse (2006) raises key questions about the uncertain relationship between (i) the intrinsic, "normal" aging process, and (ii) the clinicopathologic states represented by the labels of Alzheimer's disease (AD) and mild cognitive impairment (MCI). This short commentary offers a perspective on this (...) debate that is drawn from a consideration of underlying biological mechanisms.Because age is unquestionably the greatest single risk factor associated with AD and MCI, I begin by asking what we know about the intrinsic processes of aging. The central feature of current understanding of intrinsic aging is that it consists of the gradual, lifelong accumulation of a wide variety of molecular and cellular faults that begins very early in life and eventually leads to overt functional impairments resulting in age-related frailty, disability, and disease (Kirkwood 2005). This is an essentially bottom-up process. A strong consensus has emerged in recent years that there is no active program for aging and that there are no genetic factors that have evolved specifically to cause aging or age-related diseases. Unquestionably, there are genes that influence susceptibility to disease and even length of life, but these genes are genes for maintenance and repair functions, not for aging. It is the limitation in the past evolutionary pressure to invest in greater longevity than was required, within an environment where life was usually truncated by hazards such as starvation, injury, or infection, that means that our maintenance systems—good as they are—are insufficient to keep us going indefinitely. Added to this is the idea that there are probably also genes that program processes that are good for the young organism, but which may in later life have harmful effects. Processes like inflammation and apoptosis, which are seen to occur extensively in aged tissues, including brain, surely evolved to help cope with infection and cellular damage arising earlier in life. That they are called into play in aged tissues is a direct, but secondary, consequence of accumulated damage.With this general framework to understand the intrinsic biology of aging, let us now ask what we might expect a priori for the aging of an organ such [End Page 79] as the brain. Although we cannot pretend complete ignorance of how the brain actually does age, our enquiry can be based entirely on data from other organ systems, so we can develop our predictions about brain aging without prejudice.Aging begins very early during human development, faults accumulating from the first stages of embryonic development. Each time a cell divides, each of the daughter cells is likely to acquire a few new mutations. We know this from the estimates for the error rate in DNA replication and the size of the human genome. It is confirmed by direct evidence that at individual gene loci where mutations have been measured, mutation frequency increases with age (Morley 1998; Vijg 2000). In addition to replication errors, DNA is damaged on a daily basis to a very considerable degree by agents such as reactive oxygen species (free radicals), which are formed as byproducts of normal cellular metabolism. Although most of this damage is corrected by repair, the repair mechanisms themselves are not error free and additional mutations accumulate through this route. If a mutation is lethal to the cell, the cell dies and thus the mutation is eliminated. However, the majority of mutations are nonlethal, either because the mutation is recessive and the cell carries an intact gene copy on the other chromosome, because the gene is not currently required, or because the mutation produces only a delayed deleterious effect. Examples of genes that produce delayed deleterious effects include the genes responsible for familial AD. It is interesting to reflect that on statistical grounds alone, it is almost certain that each of us carries a randomly determined fraction of cells in our brains that bear amyloid precursor protein or presenilin mutations associated with AD. We also carry a heterogeneous array of random mutations that compromise essential cell maintenance functions. How many such... (shrink)

According to the BSM- Supergravitation Unified Theory (BSM-SG), the energy is indispensable feature of matter, while the matter possesses hierarchical levels of organization from a simple to complex forms, with appearance of fields at some levels. Therefore, the energy also follows these levels. At the fundamental level, where the primary energy source exists, the matter is in its primordial form, where two super-dense fundamental particles (FP) exist in a classical pure empty space (not a physical vacuum). They are associated with (...) the Planck scale parameters of frequency and distance and interact by Supergravitational forces. These forces are inverse proportional to the cube of distance at pure empty space and they are based on frequency interactions. Since the two FPs have different intrinsic frequencies, the SG forces appear different for interactions between the like and unlike FPs and may change the sign. This primordial form of matter exists in the super-heavy black holes located in the center of each well formed galaxy. The next upper level of matter organization includes the underlying structure of the physical vacuum, called a Cosmic Lattice, and the structure of elementary particles. They have common substructure elements obtained by specific crystallization process preceding the formation of the observable galaxies. The Cosmic Lattice, forming a space known as a physical vacuum, is responsible for the existence and propagation of the physical fields: electrical, magnetic, Newtonian gravity and inertia. The energy of physical vacuum is in two forms: Static (enormous) and Dynamic (weak). The Static energy is directly related to the Newtonian mass by the Einstein equation E = mc^2 and it is a primary source of the nuclear energy. The Dynamic energy is responsible for the existence of the electric and magnetic fields, the constant speed of light and the quantum mechanical properties of the physical vacuum. The next upper energy level is the dynamical energy of excited atoms and molecules. At this level a hidden energy wells exit, such as the internal energy of the electron and the internal energy of atoms with more than one electron. The next upper energy level is at some organic molecules and particularly in the biomolecules that contain ring atomic structures. In such a structure, some quantum states are not emitted immediately, but rotating in the ring. While in organic molecules the energy stored in such a ring is released by a chemical process, in the long chain molecule of proteins in the living organism the stored energy can be released simultaneously by triggering. A huge number of atomic rings are contained in the DNA strands. The release of the energy stored in DNA, for example, is an avalanche process that causes an emission of entangled photons possessing a strong penetrating capability. A sequence of entangled photons emitted by DNA should carry the genetic information encoded by the cordons. This mechanism, predicted in BSM-SG theory, is very important for intercommunication between the cells of the living organism. The next upper level of energy organization may exist in the brain. The brain is an organ of a most abundant number of atomic rings, while its tissue environment might permit complex energy interactions. The human brain contains billions of atomic rings. The next hypothetical upper level of energy organization is an information field, physically existed outside, but connected with the living brain. It corresponds to a specific field known as aura, while the possibility of its existence is still not accepted by the main stream science. The problem is that this field could not be detected by the currently existing technical means used for EM communications. The BSM-SG predicts that this field might differ from the EM field we use for communication, but it is a subject of a further theoretical development that must be supported by experiments using specifically designed technical means. According to the BSM-SG theory, the energy conversion from the primary energy source to the complex levels of matter and field organization is a permanent syntropic process based on complex resonance interactions. (shrink)

The paper examines the ramifications of naturalism with regard to the question of individuality in economics and biology. Economic theory has to deal with whether households, firms, and states are individuals or are mere entities such as clubs, networks, and coalitions. Biological theory has to deal with the same question with regard to cells, organisms, family packs, and colonies. To wit, the question of individuality in both disciplines involves three separate problems: the metaphysical, phenomenist, and ontological. The metaphysical problem is (...) concerned with purposeful action: Is the firm or organism exclusively the product of efficient causality (optimization) or is it motivated by final causality (purposefulness)? The phenomenist problem is interested in the substantiality of essences: Is the firm''s or organism''s scheme of institutions/traits deep or is it extraneous to identity? The ontological problem is related to the issue of reductionism: Is the behavior of lower-level organization governed by a pre-constituted entities or is it context-sensitive? The paper finds that theoretical differences run along the naturalist/anti-naturalist divide rather than along disciplinary specialization. Also, the paper finds that it is not inconsistent for the same theorist to be naturalist with regard to one problem and anti-naturalist with respect to the other two problems. (shrink)

Has science already answered the fundamental questions about the concepts of Life, Cosmos and Evolution? Has science not relegated these fundamental questions by following up on more immediate, “useful” and practical endeavors that ultimately ensure that the wheel of capitalism keeps spinning in its frantic search for material and economic progress? There is something terribly wrong with the current theory of evolution, understood as the Darwinian theory with its successive versions and extensions. The concept of natural selection, the cornerstone of (...) Darwinism, is logically inconsistent. This has been demonstrated in some of my latest academic publications. The entire conceptual framework of Darwinism is inadequate. Organisms do not compete with each other for the survival of the fittest. The fundamental relationship in Nature is not competition or confrontation, but interconnectivity, complementarity, and relational meaningfulness. A new theory of evolution is necessary to explain how it is possible that organisms as simple as bacteria, protozoa and diatoms could have generated organisms as complex as primates, and among them, the human being, a being capable of feeling and thinking, of suffering and enjoying, a being capable of having ideals and purposes. A theory that explains how it is possible that this being so complex, rich, and to some extent still unknown, has emerged from a single cell, an egg-cell, lacking all the capacities, riches and depths of human existence. Such a theory already exists. (shrink)

Neural cell adhesion molecules of the immunoglobulin superfamily are important components of the network of guidance cues and receptors that govern axon growth and guidance during development. For neural cell adhesion molecule L1, the combined application of human genetics, knockout mouse technology, and cell biology is providing fundamental insight into the role of L1 in mediating neuronal differentiation. Disease-causing mutations as well as mouse models of L1 disruption can now be used to examine the relevance of L1 (...) binding specificities and signal transduction pathways that have been observed in vitro. BioEssays 20:668–675, 1998.© 1998 John Wiley & Sons Inc. (shrink)

In this thesis, I discuss the organism's self-organization from the perspective of relational ontology. I critically examine scientific and philosophical sources that appeal to the concept of self-organization. By doing this, I aim to carry out a thorough investigation into the underlying reasons of emergent order within the ontogeny of the organism. Moreover, I focus on the relation between universal dynamics of organization and the organization of living systems. I provide a historical review of the development of (...) modern ideas related to self-organization. These ideas have been developed in relation to various research areas including thermodynamics, molecular biology, developmental biology, systems theory, and so on. In order to develop a systematic understanding of the concept, I propose a conceptual distinction between transitional self-organization and regulative self-organization. The former refers to the spontaneous emergence of order, whereas the latter refers to the self-maintaining characteristic of the living systems. I show the relation between these two types of organization within biological processes. I offer a critical analysis of various theories within the organizational approach. Several ideas and notions in these theories originate from the early studies in cybernetics. More recently, autopoiesis and the theory of biological autonomy asserted certain claims that were critical toward the ideas related to self-organization. I advocate a general theory of self-organization against these criticisms. I also examine the hierarchical nature of the organism's organization, as this is essential to understand regulative self-organization. I consider the reciprocal relation between bottom-up and top-down dynamics of organization as the basis of the organism's individuation. To prove this idea, I appeal to biological research on molecular self-assembly, pattern formation (including reaction-diffusion systems), and the self-organized characteristic of the immune system. Finally, I promote the idea of diachronic emergence by drawing support from biological self-organization. I discuss the ideas related to constraints, potentiality, and dynamic form in an attempt to reveal the emergent nature of the organism. To demonstrate the dynamicity of form, I examine research into biological oscillators. I draw the following conclusions: synchronic condition of the organism is irreducibly processual and relational, and this is the basis of the organism's potentiality for various organizational states. (shrink)