Philosophers of science have recently focused on the scientific activity of modeling phenomena, and explicated several of its properties, as well as the activities embedded into it. A first approach to modeling has been elaborated in terms of representing a target system: yet other epistemic functions, such as producing data or detecting phenomena, are at least as relevant. Additional useful distinctions have emerged, such as the one between phenomenological and mechanistic models. In biological sciences, besides mathematical models, models now come (...) in three forms: in vivo, in vitro and in silico. Each has been investigated separately, and many specific problems they raised have been laid out. Another relevant distinction is disciplinary: do models differ in significant ways according to the discipline involved—medicine or biology, evolutionary biology or earth science? Focusing on either this threefold distinction or the disciplinary boundaries reveals that they might not be sufficient from a philosophical perspective. On the contrary, focusing on the interaction between these various kinds of models, some interesting forms of explanation come to the fore, as is exemplified by the papers included in this issue. On the other hand, a focus on the use of models, rather than on their content, shows that the distinction between biological and medical models is theoretically sound. (shrink)

Conceptual analysis of health and disease is portrayed as consisting in the confrontation of a set of criteria—a “definition”—with a set of cases, called instances of either “health” or “ disease.” Apart from logical counter-arguments, there is no other way to refute an opponent’s definition than by providing counter-cases. As resorting to intensional stipulation is not forbidden, several contenders can therefore be deemed to have succeeded. This implies that conceptual analysis alone is not likely to decide between naturalism and normativism. (...) An alternative to this approach would be to examine whether the concept of disease can be naturalized. (shrink)

Since the turn of the twenty-first century, biomedical psychiatry around the globe has embraced the so-called precision medicine paradigm, a model for medical research that uses innovative techniques for data collection and analysis to reevaluate traditional theories of disease. The goal of precision medicine is to improve diagnostics by restratifying the patient population on the basis of a deeper understanding of disease processes. This paper argues that precision is ill-fitting for psychiatry for two reasons. First, in psychiatry, unlike in fields (...) like oncology, precision medicine has been understood as an attempt to improve medicine by casting out, rather than merely revising, traditional taxonomic tools. Second, in psychiatry the term “biomarker” is often used in reference to signs or symptoms that allow patients to be classified and then matched with treatments; however, in oncology “biomarker” usually refers to a disease mechanism that is useful not only for diagnostics, but also for discovering causal pathways that drug therapies can target. Given these differences between how the precision medicine paradigm operates in psychiatry and in other medical fields like oncology, while precision psychiatry may offer successful rhetoric, it is not a promising paradigm. (shrink)

Aging is an elusive property of life, and many important questions about aging depend on its definition. This article proposes to draw a definition from the scientific literature on aging. First, a broad review reveals five features commonly used to define aging: structural damage, functional decline, depletion, typical phenotypic changes or their cause, and increasing probability of death. Anything that can be called ‘aging’ must present one of these features. Then, although many conditions are not consensual instances of aging, aging (...) is consensually described as a process of loss characterized by a rate and resulting from the counteraction of protective mechanisms against mechanisms that limit lifespan. Beyond such an abstract definition, no one has yet succeeded in defining aging by a specific mechanism of aging because of an explanatory gap between such a mechanism and lifespan, a consensual explanandum of a theory of aging. By contrast, a sound theoretical definition can be obtained by revisiting the evolutionary theory of aging. Based on this theory, aging evolves thanks to the impossibility that natural selection eliminates late traits that are neutral mainly due to decreasing selective pressure. Yet, the results of physiological research suggest that this theory should be revised to also account for the small number of different aging pathways and for the existence of mechanisms counteracting these pathways, that must, on the contrary, have been selected. A synthetic, but temporary definition of aging can finally be proposed. (shrink)

In this paper, we provide a macro level analysis of the visibility of philosophy of science in the sciences over the last four decades. Our quantitative analysis of publications and citations of philosophy of science papers, published in 17 main journals representing the discipline, contributes to the longstanding debate on the influence of philosophy of science on the sciences. It reveals the global structure of relationships that philosophy of science maintains with science, technology, engineering and mathematics and social sciences and (...) humanities fields. Explored at the level of disciplines, journals and authors, this analysis of the relations between philosophy of science and a large and diversified array of disciplines allows us to answer several questions: what is the degree of openness of various disciplines to the specialized knowledge produced in philosophy of science? Which STEM and SSH fields and journals have privileged ties with philosophy of science? What are the characteristics, in terms of citation and publication patterns, of authors who get their philosophy of science papers cited outside their field? Complementing existing qualitative inquiries on the influence of specific authors, concepts or topics of philosophy of science, the bibliometric approach proposed in this paper offers a comprehensive portrait of the multiple relationships that links philosophy of science to the sciences. (shrink)

According to the received view, the transportation view, animal extrapolation consists in inductive prediction of the outcome of a mechanism in a target, based on an analogical mechanism in a model. Through an analysis of the failure of preclinical studies of TGN1412, an innovative drug, to predict the tragic consequences of its first-in-man trial in 2006, the received view is challenged by a proposed view of animal extrapolation, the chimera view. According to this view, animal extrapolation is based on a (...) hypothesis about how human organisms work, supported by the amalgamation of results drawn from various experimental organisms, and only predicting the ‘predictive grid’, that is, a global framework of the effects to be expected. (shrink)

The main thesis of this paper is that mental health practitioners can legitimately infer that a patient's given condition is a case of mental disorder without having diagnosed any specific mental disorder. The article shows how this is justifiable by relying either on psychopathological reasoning, on 'intentional' analysis or possibly on other modes of reasoning. In the end, it highlights the clinical and philosophical consequences of the plurality of modes of 'inferences to mental disorder'.

Science starts by using terms such as ‘temperature’ or ‘fish’ or ‘gene’ to preliminarily delimitate the extension of a phenomenon, and concludes by giving most of them a technical meaning based on an explanatory model. This transforma- tion of the meaning of the term is an essential part of its naturalization. Debating on the definition of ‘disease’, what most philosophers of medicine have examined is the pre-naturalized meaning of the term: for that reason they have focused on the task of (...) delimiting disease and non-disease (health), mainly used conceptual analysis as a method of choice, and considered the nosological level of ‘disease judgments’ rather than the pathophysiological or psychopathological level of disease mechanisms, thus making them impervious to most scientific discoveries. By focusing instead on the naturalized concept of disease and following some suggestions by philosophers of biology and scientists in cutting-edge fields of biomedical research, they could gar- ner results from a comparison of the mechanisms of diseases. This would ultimately result in a general theory of disease linked with our most general theories on living beings, among them, systems biology and network medicine. Before undertaking such a task, preliminary questions arise: is it likely that there are biological features common to different types of disease? Is it a philosopher’s job to determine what they consist in? What use would such a general theoretical definition of disease be? (shrink)

Despite its vagueness Personalized, Precision, P4, P5, individualized, stratified medicine—or p-medicine in short—has become an increasingly popular term in biomedical literature. Philosophers have attempted to analyze what these various terms involve and have discussed consequences for medical practices. In this article, I argue that an important question remains unaddressed: what has made this project of p-medicine convincing to so many? My argument is that without real achievements, it would never have been. I also make the case that these achievements stem (...) from the domain of monoclonal antibodies, a new type of drug that justifies talks of personalized, precise, stratified, etc., medicine. In conclusion, while it may be possible to label any projection in the future of medicine as ‘p-medicine’, it is impossible to overlook mab-medicine as the spearhead. (shrink)

English summary: Based on the famous essay by Georges Canguilhem on what is normal and pathological (originally published in 1943), extensive philosophical literature (mainly Anglo-Saxon) has attempted to define these concepts and analyze their status. The main discussion focuses on the following question: can you describe health and illness as natural phenomena or are they states that are determined by values? French text. French description: Depuis le celebre essai de Georges Canguilhem sur le normal et le pathologique publie initialement en (...) 1943 et dont l'un des objectifs etait la clarification des concepts de sante et de maladie, une litterature philosophique abondante, principalement anglo-saxonne, s'est attachee a definir ces concepts et a analyser leur statut. Le principal debat de ce domaine emergent de la philosophie de la medecine porte sur la question: peut-on decrire la sante et la maladie comme des phenomenes naturels ou s'agit-il d'etats qui sont determines par des valeurs? Tous les textes presentes dans ce volume ont participe de cette controverse. Ceux de la premiere section accordent une part importante a la composante biologique. Ceux de la seconde donnent le primat a la notion d'action. Ceux de la derniere section mettent en question l'utilite ou la possibilite meme de definir les deux concepts. (shrink)

Philosophers of science have recently focused on the scientific activity of modeling phenomena, and explicated several of its properties, as well as the activities embedded into it. A first approach to modeling has been elaborated in terms of representing a target system: yet other epistemic functions, such as producing data or detecting phenomena, are at least as relevant. Additional useful distinctions have emerged, such as the one between phenomenological and mechanistic models. In biological sciences, besides mathematical models, models now come (...) in three forms: in vivo, in vitro and in silico. Each has been investigated separately, and many specific problems they raised have been laid out. Another relevant distinction is disciplinary: do models differ in significant ways according to the discipline involved—medicine or biology, evolutionary biology or earth science? Focusing on either this threefold distinction or the disciplinary boundaries reveals that they might not be sufficient from a philosophical perspective. On the contrary, focusing on the interaction between these various kinds of models, some interesting forms of explanation come to the fore, as is exemplified by the papers included in this issue. On the other hand, a focus on the use of models, rather than on their content, shows that the distinction between biological and medical models is theoretically sound. (shrink)

Following the neurophenomenological approach, we propose a model of emotional emergence that identifies the experimental structures of time involved in emotional experience and their plausible components in terms of cognition, physiology, and neuroscience. We argue that surprise, as a lived experience, and its physiological correlates of the startle reflex and cardiac defense are the core of the dynamic, and that the heart system sets temporally in motion the dynamic of emotional emergence. Finally, in reference to Craig’s model of emotion, we (...) propose an integrative model of the temporal dynamic of emotional emergence that allows emotions to be distinguished depending on each temporal phase and that involves the following three systems: the brain , the consciousness , and the doubled-sided continuum of the body-heart context, with the heart as the focus within the body during emotion. This model provides the framework for future developments in 1st- and 3rd-person approaches for an integrative understanding of the science of emotion, including the fields of psychophysiology and psychopathology. (shrink)

In our commentary on Lynch et al.’s target paper, we focus on decomposition as a research strategy. We argue that not only the presumptive microbial causes but also their supposed phenotypic effects need to be decomposed relative to each other. Such a dual decomposition strategy ought to improve the way in which causal claims in microbiome research can be made and understood.

In our commentary on Lynch et al.’s target paper, we focus on decomposition as a research strategy. We argue that not only the presumptive microbial causes but also their supposed phenotypic effects need to be decomposed relative to each other. Such a dual decomposition strategy ought to improve the way in which causal claims in microbiome research can be made and understood.

In our commentary on Lynch et al.’s target paper, we focus on decomposition as a research strategy. We argue that not only the presumptive microbial causes but also their supposed phenotypic effects need to be decomposed relative to each other. Such a dual decomposition strategy ought to improve the way in which causal claims in microbiome research can be made and understood.

M. Henry voit à tort chez Maine de Biran la distinction entre trois figures du corps propre: corps objectif (extérieur et mondain), corps organique (terme résistant de l'effort), et corps subjectif (confondu avec l'ego). Maine de Biran distingue bien trois corps, mais le troisième, loin d'être confondu avec l'ego, est un corps de pure passivité duquel l'ego est absent. Cet état d'affectivité pure étudié par Biran répond à la critique par M. Henry de sa théorie de la passivité, et corrige (...) la théorie de l'auto-affection. M. Henry misunderstands Maine de Biran's distinction between three dimensions of the body: while the former makes a difference between the objective body (in the external world), the organic body (resistant term of the effort), and the subjective body (identified with the ego), the latter considers the third to be a body of mere passivity from which the ego is absent. The description Biran makes of this state of pure sensitivity answers M. Henry's critique of his theory of passivity, and modifies the theory of « auto-affection ». (shrink)

Philosophers of biology usually distinguish historical and systemic accounts of functions. In many areas of experimental biology the "systemic" account is often the most relevant. Yet there are problems this account does admittedly not face up to very well. My contention is that, though two minor problems are irredeemably unsolvable for the systemic account of function, the major ones can be solved by assuming that 'function' denotes (directly) a causal role in a model and (indirectly) the corresponding process in nature. (...) I try to show this through the analysis of the hypothalamus-pituitary-adrenal axis of stress. (shrink)

La médecine ne se contente pas de diagnostiquer et de traiter des maladies : elle vise aussi à les expliquer. En cela, elle prend pied de plein droit dans le domaine de la science. En quoi consistent les explications médicales, et qu'est-ce qui les singularise au sein des explications en biologie? La première caractéristique des explications médicales est leur pluralité. La médecine semble en effet réunir sous un même label des explications très diverses, voire hétérogènes, unies seulement par l'objet d'application (...) et la visée thérapeutique. Le propre de l'explication scientifique médicale, c'est sa pluridisciplinarité.Un canevas théorique est nécessaire pour mettre en évidence ce qui, dans une explication scientifique, peut permettre une telle diversité des explications. Celui-ci est fourni par la notion de " valeur explicative " : une croyance, injustifiable, mais bien fondée, en l'exhaustivité des conditions initiales dont une explication doit tenir compte. Bien qu'elle tende par elle-même à tout expliquer sans reste, et qu'elle exclut du domaine disciplinaire qu'elle définit ainsi tout autre type d'explication, une valeur explicative n'exclut jamais en droit la possibilité d'explications scientifiques d'autres types. Un nombre indéfini de valeurs explicatives, exclusives les unes des autres, fondatrices de domaines scientifiques distincts, est donc possible. La médecine présente ainsi la particularité de rassembler plusieurs valeurs explicatives différentes et qui plus est, de les contraindre à la convergence ou à la collaboration. Quelques-unes des principales valeurs explicatives de la médecine sont présentées, de même que les enjeux de leur confrontation. Clinique, épidémiologique, mécanique, génétique, cytologique, infectiologique, pharmacologique, l'explication médicale se fonde à chaque fois sur une manière différente de considérer le phénomène pathologique. (shrink)

Because biologization of psychiatric constructs does not involve derivation of laws, or reduce the number of entities involved, the traditional term of ‘reduction’ should be replaced. This paper describes biologization in terms of redefinition, which involves changing the definition of terms sharing the same extension. Redefinition obtains through triangulation and calibration, that is, respectively, detection of an object from two different spots, and tweaking parameters of detection in order to optimize the picture. The unity of the different views of the (...) same object does not occur through derivation from one of them, as reduction suggests, nor does it obtain through mechanistic unity or the goal of explaining one mechanism, as the phrase ‘mosaic unity’ suggests. Instead, it depends on finding a specific angle of observation, from which linguistic consistency matches sound localization in the brain, so that all observations make sense together, just as an anamorphic picture makes clear sense only when observed from the right spot. (shrink)

Contrairement aux idées reçues, Hegel n’est pas un précurseur de la pensée totalitaire, auquel on pourrait opposer un Bergson républicain et démocrate. Tous deux parlent de la communauté politique comme d’un organisme, doctrine affectionnée du totalitarisme. Ni chez l’un, ni chez l’autre, on ne peut atténuer la portée de l’affirmation en invoquant un usage métaphorique : il faut entendre, chez l’un comme chez l’autre, l’organisme au sens propre mais large. L’organicité du politique, loin de la menacer, est la seule forme (...) compatible avec la liberté des individus, grâce à la distinction que l’on peut faire entre organisation toute faite et organisation se faisant : si la première traite les individus en rouages d’un mécanisme, la seconde est l’expression immédiate de l’épanouissement de leurs libertés.Popper wrote that Hegel, as a thinker, is a forerunner of totalitarianism ; on the other hand, one cannot but regard Bergson as a true democrat. Both however considered the politic body as an organism, a doctrine supporters of the totalitarian state favoured. The assertion must not be underrated : neither thinker intended to use a metaphorical expression, hence a broad meaning of « organism ». As a matter of fact the organicity of a politic body, far from threatening individual freedom, is the only form that proves compatible with individuality. The important thing is to distinguish all-made « organized organisation » from selfmaking « organizing organisation » : the former treats individuals as mechanical entities, while the latter is the result of the self-development of their freedom. (shrink)

La conception traditionnelle des théories scientifiques en philosophie de langue anglaise, qu’on appelle la « received view », et qui culmine au début des années 1960, posait de nombreux obstacles à une conception des théories scientifiques en biologie et en médecine. La conception sémantique des théories scientifiques qui lui succéda permit de lever ces obstacles, mais pas de différencier les théories en biologie expérimentale et en médecine. Le présent article met en évidence comment, en s’appuyant sur cette conception, Schaffner établit (...) la spécificité des théories biologiques et médicales par rapport aux théories physiques, comment Thompson établit que c’est le savoir biologique et non le savoir clinique qui, véritablement théorique, fonde le caractère proprement scientifique de la médecine, et enfin, comment Sadegh-Zadeh peut proposer à son tour des caractéristiques des théories médicales qui leur sont potentiellement spécifiques et les distinguent des théories biologiques. (shrink)

If the healthy and the pathological are not merely judgments qualifiers, but real phenomena, it must be possible to define both of them positively, which, in this context, means as factual contraries. On the other hand, only a privative definition, either of the pathological as 'non-healthy', or of the healthy as 'non-pathological', can rationally circumscribe all possible states of an organism. This fluctuation between two meanings of the 'healthy'-'pathological' opposition, factual vs. rational, characterizes the ordinary usage of these concepts and (...) puts all philosophical definitions in a hopeless situation. Although a scientific definition may conceal this equivocation by adequately setting out the terms of the problem of discriminating between the 'healthy' and the 'pathological', it could explain some of the difficulties met in determining 'gold standards', in the choice of separators, and in the assessment of the diagnostic qualities of tests. (shrink)

If the healthy and the pathological are not merely judgments qualifiers, but real phenomena, it must be possible to define both of them positively, which, in this context, means as factual contraries. On the other hand, only a privative definition, either of the pathological as ‘non-healthy’, or of the healthy as ‘non-pathological’, can rationally circumscribe all possible states of an organism. This fluctuation between two meanings of the ‘healthy’–‘pathological’ opposition, factual vs. rational, characterizes the ordinary usage of these concepts and (...) puts all philosophical definitions in a hopeless situation. Although a scientific definition may conceal this equivocation by adequately setting out the terms of the problem of discriminating between the ‘healthy’ and the ‘pathological’, it could explain some of the difficulties met in determining ‘gold standards’, in the choice of separators, and in the assessment of the diagnostic qualities of tests. (shrink)

We discuss the latent variables construct, particularly in regard to the following: that latent variables are considered as the sole explanatory factor of a disorder; that pragmatic concerns are ignored; and that the relationship of these variables to biological markers is not addressed. Further, we comment on the relationship between bridge symptoms and causality, and discuss the proposal in relationship to other constructs (endophenotypes, connectionist-inspired networks).

Unlike inert objects, organisms and their cells have the ability to initiate activity by themselves and thus change their properties or states even in the absence of an external cause. This crucial difference led us to search for principles suitable for the study organisms. We propose that cells follow the default state of proliferation with variation and motility, a principle of biological inertia. This means that in the presence of sufficient nutrients, cells will express their default state. We also propose (...) a principle of variation that addresses two central features of organisms, variation and historicity. To address interdependence between parts, we use a third principle, the principle of organization, more specifically, the notion of the closure of constraints. Within this theoretical framework, constraints are specific theoretical entities defined by their relative stability with respect to the processes they constrain. Constraints are mutually dependent in an organized system and act on the default state.Here we discuss the application and articulation of these principles for mathematical modeling of morphogenesis in a specific case, that of mammary ductal morphogenesis, with an emphasis on the default state. Our model has both a biological component, the cells, and a physical component, the matrix that contains collagen fibers. Cells are agents that move and proliferate unless constrained; they exert mechanical forces that act (i) on collagen fibers and (ii) on other cells. As fibers are organized, they constrain the cells’ ability to move and to proliferate. This model exhibits a circularity that can be interpreted in terms of the closure of constraints. Implementing our mathematical model shows that constraints to the default state are sufficient to explain the formation of mammary epithelial structures. Finally, the success of this modeling effort suggests a stepwise approach whereby additional constraints imposed by the tissue and the organism can be examined in silico and rigorously tested by in vitro and in vivo experiments, in accordance with the organicist perspective we embrace. (shrink)

We characterize access to empirical objects in biology from a theoretical perspective. Unlike objects in current physical theories, biological objects are the result of a history and their variations continue to generate a history. This property is the starting point of our concept of measurement. We argue that biological measurement is relative to a natural history which is shared by the different objects subjected to the measurement and is more or less constrained by biologists. We call symmetrization the theoretical and (...) often concrete operation which leads to considering biological objects as equivalent in a measurement. Last, we use our notion of measurement to analyze research strategies. Some strategies aim to bring biology closer to the epistemology of physical theories, by studying objects as similar as possible, while others build on biological diversity. (shrink)

Emotive speech is a social act in which a speaker displays emotional signals with a specific intention; in the case of third-party complaints, this intention is to elicit empathy in the listener. The present study assessed how the emotivity of complaints was perceived in various conditions. Participants listened to short statements describing painful or neutral situations, spoken with a complaining or neutral prosody, and evaluated how complaining the speaker sounded. In addition to manipulating features of the message, social-affiliative factors which (...) could influence complaint perception were varied by adopting a cross-cultural design: participants were either Québécois or French and listened to utterances expressed by both cultural groups. The presence of a complaining tone of voice had the largest effect on participant evaluations, while the nature of statements had a significant, but smaller influence. Marginal effects of culture on explicit evaluation of complaints were found. A multiple mediation analysis suggested that mean fundamental frequency was the main prosodic signal that participants relied on to detect complaints, though most of the prosody effect could not be linearly explained by acoustic parameters. These results highlight a tacit agreement between speaker and listener: what characterizes a complaint is how it is said, more than what it is about or who produces it. More generally, the study emphasizes the central importance of prosody in expressive speech acts such as complaints, which are designed to strengthen social bonds and supportive responses in interactive behavior. This intentional and interpersonal aspect in the communication of emotions needs to be further considered in research on affect and communication. (shrink)

In Western countries today, a growing number of women delay motherhood until their late 30s and even 40s, as they invest time in pursuing education and career goals before starting a family. This social trend results from greater gender equality and expanded opportunities for women and is influenced by the availability of contraception and assisted reproductive technologies. However, advanced maternal age is associated with increased health risks, including infertility. While individual medical solutions such as ART and elective egg freezing can (...) promote reproductive autonomy, they entail significant risks and limitations. We thus argue that women should be better informed regarding the risks of advanced maternal age and ART, and that these individual solutions need to be supplemented by a public health approach, including policy measures that provide women with the opportunity to start a family earlier in life without sacrificing personal career goals. (shrink)

Zeno’s paradoxes of motion, allegedly denying motion, have been conceived to reinforce the Parmenidean vision of an immutable world. The aim of this article is to demonstrate that these famous logical paradoxes should be seen instead as paradoxes of immobility. From this new point of view, motion is therefore no longer logically problematic, while immobility is. This is convenient since it is easy to conceive that immobility can actually conceal motion, and thus the proposition “immobility is mere illusion of the (...) senses” is much more credible than the reverse thesis supported by Parmenides. Moreover, this proposition is also supported by modern depiction of material bodies: the existence of a ceaseless random motion of atoms—the ‘thermal agitation’—in the scope of contemporary atomic theory, can offer a rational explanation of this ‘illusion of immobility’. Our new approach to Zeno’s paradoxes therefore leads to presenting the novel concept of ‘impermobility’, which we think is a more adequate description of physical reality. (shrink)

To those who have observed it for a long time, the People's Republic of China today has the appearance of a convalescent who has made his way back from a long illness and is slowly relearning to use his vital organs. And this is the consequence of the decisive and remarkable measures taken after the death of Mao Tse-tung and the subsequent elimination of his abusive widow, Chiang Ch'ing, by survivors of the great cultural revolution, now in the upper circles (...) of the Chinese Communist party. Explanations were provided in the “Resolution on the History of the Chinese Communist Party” adopted June 27, 1981, at the Sixth Plenary Session of the Central Committee of the Eleventh Party Congress. But the real turning point dates from 1978, in the historic third session of this same Eleventh Congress when the opposition to Mao's chosen successor, Hua Guo-feng, called upon participants to “liberate their minds and to seek truth in the facts”. A new People's China had begun to take shape, and although it is not yet possible to pass judgement on its future prospects, visitors who travel there today can only bear witness to the return of this immense population to existential reality, while little by little the “barracks socialism” of the ultra-leftists is dying out. (shrink)

This authored monograph introduces a genuinely theoretical approach to biology. Starting point is the investigation of empirical biological scaling including their variability, which is found in the literature, e.g. allometric relationships, fractals, etc. The book then analyzes two different aspects of biological time: first, a supplementary temporal dimension to accommodate proper biological rhythms; secondly, the concepts of protension and retention as a means of local organization of time in living organisms. Moreover, the book investigates the role of symmetry in biology, (...) in view of its ubiquitous importance in physics. In relation with the notion of extended critical transitions, the book proposes that organisms and their evolution can be characterized by continued symmetry changes, which accounts for the irreducibility of their historicity and variability. The authors also introduce the concept of anti-entropy as a measure for the potential of variability, being equally understood as alterations in symmetry. By this, the book provides a mathematical account of Gould's analysis of phenotypic complexity with respect to biological evolution. The target audience primarily comprises researchers interested in new theoretical approaches to biology, from physical, biological or philosophical backgrounds, but the book may also be beneficial for graduate students who want to enter this field. (shrink)

We provide a new perspective on the relation between the space of description of an object and the appearance of novelties. One of the aims of this perspective is to facilitate the interaction between mathematics and historical sciences. The definition of novelties is paradoxical: if one can define in advance the possibles, then they are not genuinely new. By analyzing the situation in set theory, we show that defining generic (i.e., shared) and specific (i.e., individual) properties of elements of a (...) set are radically different notions. As a result, generic and specific definitions of possibilities cannot be conflated. We argue that genuinely stating possibilities requires that their meaning has to be made explicit. For example, in physics, properties playing theoretical roles are generic; then, generic reasoning is sufficient to define possibilities. By contrast, in music, we argue that specific properties matter, and generic definitions become insufficient. Then, the notion of new possibilities becomes relevant and irreducible. In biology, among other examples, the generic definition of the space of DNA sequences is insufficient to state phenotypic possibilities even if we assume complete genetic determinism. The generic properties of this space are relevant for sequencing or DNA duplication, but they are inadequate to understand phenotypes. We develop a strong concept of biological novelties which justifies the notion of new possibilities and is more robust than the notion of changing description spaces. These biological novelties are not generic outcomes from an initial situation. They are specific and this specificity is associated with biological functions, that is to say, with a specific causal structure. Thus, we think that in contrast with physics, the concept of new possibilities is necessary for biology. (shrink)

A survey is given of the concepts of interaction (force) and matter, i.e., of process and substance. The development of these concepts, first in antiquity, then in early modern times, and finally in the contemporary system of quantum field theory is described. After a summary of the basic phenomenological attributes (coupling strengths, symmetry quantities, charges), the common ground of concepts of quantum field theory for both interactions and matter entities is discussed. Then attention is focused on the gauge principle which (...) has been developed to describe all interaction fields in the same way, and hopefully to unite them all into one unified field. While a similar unification of all fundamental types of matter fields (quarks and leptons) into one family may be possible (SU 5), there still remains at this level a duality between interaction quanta (bosons with spin 1) and matter particles (fermions with spin 1/2). Whether this duality may be removed in some future supersymmetric theory is not discussed in this paper. Nor is Quantum Gravitation discussed, though the analogy of the gauge principle for the three fundamental non-gravitational interactions (hadronic, electromagnetic and weak) to Einstein's principle of equivalence for gravitation in spacetime is noted. However, the equivalence concept is applied not to spacetime but to the internal spaces for the matter (or charge) fields which are the sources between which the fundamental interactions operate. The gauge principle states that a change in the measures of the internal space charge of gauge or phases of the matter fields is equivalent to, and can be compensated by, suitably introduced interaction fields. From such an interaction field, the gauge potential field in the internal space, one may derive a gauge force field by exterior differentiation.Geometrically, the collection of all internal spaces, one over each point of spacetime, constitutes a fiber bundle. The gauge potential field represents a connection on the fiber bundle, and the gauge force field is the curvature (calculated by taking the exterior derivative of the connection and adding to it the exterior product of the connection with itself). Thus, just as gravitational force is interpreted as spacetime curvature, so the three other fundamental forces are interpretable as internal space curvature. The Standard Model which unites the three non-gravitational fields into an SU c 3 ×SU 2×U 1 structure, and the grand unified model, SU 5, are discussed briefly, and difficulties are noted. Finally it is suggested that a composite model, based on more subtle structure, may be needed to remove the present obscurities and difficulties that stand in the way of a unified theory. (shrink)

The Anthropocene crisis is frequently described as the rarefaction of resources or resources per capita. However, both energy and minerals correspond to fundamentally conserved quantities from the perspective of physics. A specific concept is required to understand the rarefaction of available resources. This concept, entropy, pertains to energy and matter configurations and not just to their sheer amount. However, the physics concept of entropy is insufficient to understand biological and social organizations. Biological phenomena display both historicity and systemic properties. A (...) biological organization, the ability of a specific living being to last over time, results from history, expresses itself by systemic properties, and may require generating novelties The concept of anti-entropy stems from the combination of these features. We propose that Anthropocene changes disrupt biological organizations by randomizing them, that is, decreasing anti-entropy. Moreover, second-order disruptions correspond to the decline of the ability to produce functional novelties, that is, to produce anti-entropy. (shrink)

It is commonly believed that there is no equivalent of the Church–Turing thesis for computation over the reals. In particular, computational models on this domain do not exhibit the convergence of formalisms that supports this thesis in the case of integer computation. In the light of recent philosophical developments on the different meanings of the Church–Turing thesis, and recent technical results on analog computation, I will show that this current belief confounds two distinct issues, namely the extension of the notion (...) of effective computation to the reals on the one hand, and the simulation of analog computers by Turing machines on the other hand. I will argue that it is possible in both cases to defend an equivalent of the Church–Turing thesis over the reals. Along the way, we will learn some methodological caveats on the comparison of different computational models, and how to make it meaningful. (shrink)

The analogy between living beings and computers was introduced with circumspection by Schrödinger and has been widely propagated since, rarely with a precise technical meaning. Critics of this perspective are numerous. We emphasize that this perspective is mobilized to justify what may be called a regressive reductionism by comparison with physics or the Cartesian method. Other views on the living are possible, and we focus on an epistemological and theoretical framework where historicity is central, and the regularities susceptible to mathematization (...) are constraints whose existence is fundamentally precarious and historically contingent. We then propose to reinterpret the computer, no longer as a Turing machine but as constituted by constraints. This move allows us to understand that computation in the sense of Church-Turing is only a part of the theoretical determination of what actually happens in a computer when considering them in their larger theoretical context where historicity is also central. (shrink)