The title of the present book suggests that scientific results obtained in mathematics and quantum physics can be in some way related to the question of the existence of God. This seems possible to us, because it is our conviction that reality in all its dimensions is intelligible. The really impressive progress in science and technology demonstrates that we can trust our intellect, and that nature is not offering us a collection of meaningless absurdities. We first of all intend to (...) show with results taken from mathematics and quantum physics: Mathematical Undecidability: man will never have a universal method to solve any mathematical problem. In arithmetic there always will be unsolved, solvable problems. Quantum Nonlocality: certain phenomena in nature seem to imply the existence of correlations based on faster-than-light influences. These influences, however, are not accessible to manipulation by man for use in, for example, faster than light communication. In the various contributions pieces of a puzzle are offered, which suggest that there exists more than the world of phenomena around us. The results discussed point to intelligent and unobservable causes governing the world. One is led to perceive the shade of a reality which many people would call God. (shrink)

We discuss models that attempt to provide an explanation for the violation of Bell inequalities at a distance in terms of hidden influences. These models reproduce the quantum correlations in most situations, but are restricted to produce local correlations in some configurations. The argument presented in (Bancal et al. Nat Phys 8:867, 2012) applies to all of these models, which can thus be proved to allow for faster-than-light communication. In other words, the signalling character of these models cannot remain hidden.

Symbiosis plays a fundamental role in contemporary biology, as well as in recent thinking in philosophy of biology. The discovery of the importance and universality of symbiotic associations has brought new light to old debates in the field, including issues about the concept of biological individuality. An important aspect of these debates has been the formulation of the hologenome concept of evolution, the notion that holobionts are units of natural selection in evolution. This review examines the philosophical assumptions that underlie (...) recent proposal of the hologenome concept of evolution, and traces those debates back in time to their historical origins, to the moment when the connection between the topics of symbiosis and biological individuality first caught the attention of biologists. The review is divided in two parts. The first part explores the historical origins of the connection between the notion of symbiosis and the concept of biological individuality, and emphasizes the role of A. de Bary, R. Pound, A. Schneider and C. Merezhkowsky in framing the debate. The second part examines the hologenome concept of evolution and explores four parallelisms between contemporary debates and the debates presented in the first part of the essay, arguing that the different debates raised by the hologenome concept were already present in the literature. I suggest that the novelty of the hologenome concept of evolution lies in the wider appreciation of the importance of symbiosis for maintaining life on Earth as we know it. Finally, I conclude by suggesting the importance of exploring the connections among contemporary biology, philosophy of biology and history of biology in order to gain a better understanding of contemporary biology. (shrink)

Holobionts are symbiotic assemblages composed by a host plus its microbiome. The status of holobionts as individuals has recently been a subject of continuous controversy, which has given rise to two main positions: on the one hand, holobiont advocates argue that holobionts are biological individuals; on the other, holobiont detractors argue that they are just mere chimeras or ecological communities, but not individuals. Both parties in the dispute develop their arguments from the framework of the philosophy of biology, in terms (...) of what it takes for a “conglomerate” to be considered an interesting individual from a biological point of view. However, the debates about holobiont individuality have important ontological implications that have remained vaguely explored from a metaphysical framework. The purpose of this paper is to cover that gap by presenting a metaphysical approach to holobionts individuality. Drawing upon a conception of natural selection that puts the focus on the transgenerational recurrence of the traits and that supports the thesis that holobionts are units of selection, we argue that holobionts bear emergent traits and exert downward powers over the entities that compose them. In this vein, we argue, a reasonable argument can be made for conceiving holobionts as emergent biological individuals. (shrink)

Bourrat and Griffiths :33, 2018) have recently argued that most of the evidence presented by holobiont defenders to support the thesis that holobionts are evolutionary individuals is not to the point and is not even adequate to discriminate multispecies evolutionary individuals from other multispecies assemblages that would not be considered evolutionary individuals by most holobiont defenders. They further argue that an adequate criterion to distinguish the two categories is fitness alignment, presenting the notion of fitness boundedness as a criterion that (...) allows divorcing true multispecies evolutionary individuals from other multispecies assemblages and provides an adequate criterion to single out genuine evolutionary multispecies assemblages. A consequence of their criterion is that holobionts, as conventionally defined by hologenome defenders, are not evolutionary individuals except in very rare cases, and for very specific host-symbiont associations. This paper is a critical response to Bourrat and Griffiths’ arguments and a defence of the arguments presented by holobiont defenders. Drawing upon the case of the hologenomic basis of the evolution of sanguivory in vampire bats, I argue that Bourrat and Griffiths overlook some aspects of the biological nature of the microbiome that justifies the thesis that holobionts are evolutionarily different to other multispecies assemblages. I argue that the hologenome theory of evolution should not define the hologenome as a collection of genomes, but as the sum of the host genome plus some traits of the microbiome which together constitute an evolutionary individual, a conception I refer to as the stability of traits conception of the hologenome. Based on that conception I argue that the evidence presented by holobiont defenders is to the point, and supports the thesis that holobionts are evolutionary individuals. In this sense, the paper offers an account of the holobiont that aims to foster a dialogue between hologenome advocates and hologenome critics. (shrink)

For Van Rensselaer Potter (1911–2001), Global Bio-Ethics is about building on the legacy of Aldo Leopold (1887–1948), one of the most notable forest managers of the twentieth century who brought to light the importance of pragmatism in the sciences and showed us a new way to proceed with environmental ethics. Following Richard Huxtable and Jonathan Ives's methodological 'Framework for Empirical Bioethics Research Projects' called 'Mapping, framing, shaping,' published in BMC Medicine Ethics (2019)), we propose operationalizing a framework for Global Bio-Ethics (...) by hybridizing approaches in empirical bioethics and ecosystem management. We explain this framework using the metaphor of forest management. This mixed approach is articulated through three phases: (1) mapping the “landscape” to build a working theory, (2) framing the “scene” to prepare the fieldwork, and (3) shaping bioethics “tools” to stimulate cooperation. Applying this methodology, an adaptive management cycle is outlined to help ensure that political processes are sustainable and socially acceptable, still based on strategic and ethical thinking, but also capable of reshaping failing policies. (shrink)

Contemporary biological research has suggested that some host–microbiome multispecies systems (referred to as “holobionts”) can in certain circumstances evolve as unique biological individual, thus being a unit of selection in evolution. If this is so, then it is arguably the case that some biological adaptations have evolved at the level of the multispecies system, what we call hologenomic adaptations. However, no research has yet been devoted to investigating their nature, or how these adaptations can be distinguished from adaptations at the (...) species-level (genomic adaptations). In this paper, we cover this gap by investigating the nature of hologenomic adaptations. By drawing on the case of the evolution of sanguivory diet in vampire bats, we argue that a trait constitutes a hologenomic adaptation when its evolution can only be explained if the holobiont is considered the biological individual that manifests this adaptation, while the bacterial taxa that bear the trait are only opportunistic beneficiaries of it. We then use the philosophical notions of emergence and inter-identity to explain the nature of this form of individuality and argue why it is special of holobionts. Overall, our paper illustrates how the use of philosophical concepts can illuminate scientific discussions, in the trend of what has recently been called metaphysics of biology. (shrink)

This paper aims to offer a new argument in defence bacterial species pluralism. To do so, I shall first present the particular issues derived from the conflict between the non-theoretical understanding of species as units of classification and the theoretical comprehension of them as units of evolution. Secondly, I shall justify the necessity of the concept of species for the bacterial world, and show how medicine and endosymbiotic evolutionary theory make use of different concepts of bacterial species due to their (...) distinctive purposes. Finally, I shall show how my argument provides a new source of defence for bacterial pluralism. (shrink)

Philippe Huneman has recently questioned the widespread application of mechanistic models of scientific explanation based on the existence of structural explanations, i.e. explanations that account for the phenomenon to be explained in virtue of the mathematical properties of the system where the phenomenon obtains, rather than in terms of the mechanisms that causally produce the phenomenon. Structural explanations are very diverse, including cases like explanations in terms of bowtie structures, in terms of the topological properties of the system, or in (...) terms of equilibrium. The role of mathematics in bowtie structured systems and in topologically constrained systems has recently been examined in different papers. However, the specific role that mathematical properties play in equilibrium explanations requires further examination, as different authors defend different interpretations, some of them closer to the new-mechanistic approach than to the structural model advocated by Huneman. In this paper, we cover this gap by investigating the explanatory role that mathematics play in Blaser and Kirschner’s nested equilibrium model of the stability of persistent long-term human-microbe associations. We argue that their model is explanatory because: i) it provides a mathematical structure in the form of a set of differential equations that together satisfy an ESS; ii) that the nested nature of the ESSs makes the explanation of host-microbe persistent associations robust to any perturbation; iii) that this is so because the properties of the ESS directly mirror the properties of the biological system in a non-causal way. The combination of these three theses make equilibrium explanations look more similar to structural explanations than to causal-mechanistic explanation. (shrink)

This paper revisits the debate over whether the study of facilitation requires ecologists to revise their understanding of the relationship between realized and fundamental niches as conceptualized by Hutchinson. Following Rodriguez-Cabal et al., I argue against Bruno et al.’s claim that facilitation can make a species’ realized niche larger than its fundamental niche. However, I also maintain that the abstract Hutchinsonian conceptualization of the niche makes a whole range of facilitative interactions—which I propose to call ameliorative facilitation—invisible to niche-based approaches (...) to the study of ecological communities. I propose a way to incorporate ameliorative facilitation into such approaches. My proposal involves supplementing the Hutchinsonian realized/fundamental dyad with a third concept: the potential niche. This concept was introduced by ecologists studying the effects of environmental change on species distributions, but I show how it could also be fruitfully used in facilitation studies. I argue that this proposed solution is more appealing than Stachowicz’s suggestion that Hutchinson’s realized/fundamental contrast be applied to a spatial-geographical, as opposed to an abstract-conceptual, notion of the niche. (shrink)

The hologenome concept of evolution is a hypothesis about the evolution of animals and plants. It asserts that the evolution of animals and plants was partially triggered by their interactions with their symbiotic microbiomes. In that vein, the hologenome concept posits that the holobiont (animal host + symbionts of the microbiome) is a unit of selection. -/- The hologenome concept has been severely criticized on the basis that selection on holobionts would only be possible if there were a tight transgenerational (...) host-genotype-to-symbiont-genotype connection. As our current evidence suggests that this is not the case for most of the symbiont species that compose the microbiome of animals and plants, the opportunity for holobiont selection is very low in relation to the opportunity for selection on each of the species that compose the host microbiome. Therefore, holobiont selection will always be disrupted ‘from below’, by selection on each of the species that compose the microbiome. -/- This thesis constitutes a conceptual effort to defend philosophically the hologenome concept. I argue that the criticism according to which holobiont selection requires tight transgenerational host-genotype-to-symbiont-genotype connection is grounded on a metaphysical view of the world according to which the biological hierarchy needs to be nested, such that each new level of selection includes every entity from below. Applied to hologenomes, it entails that the hologenome is a collection of genomes, and selection of hologenomes is assumed to entail cospeciation of the host with the species that constitute its microbiome. -/- Against that interpretation, I propose the ‘stability of traits’ account, according to which hologenome evolution is the result of the action of natural selection in a non-nested hierarchical world. In that vein, hologenome evolution does not entail cospeciation, and thus it does not require tight transgenerational host-genotype-to-symbiont-genotype connection. By embracing a multilevel selection perspective, I argue that hologenome evolution results from the simultaneous action of natural selection on each of the lineages that compose the microbiome, and on the assemblage composed by the host genome plus the functional traits of its microbiome. Hologenome selection occurs when the evolution of the traits of the microbiome result from their effects on the fitness of the host, and it can take the form of multilevel selection 1, or multilevel selection 2. In both cases, hologenome selection entails the evolution of microbiome traits, as well as evolution of the host genome, rather than cospeciation of lineages. (shrink)

This paper discusses Millstein’s criticism of the consensus view formed against selected-effects ecological functions. I argue that Millstein’s defense of coevolution-based selected-effects ecological functions applies to a notion of function as an activity, whereas proponents of the consensus view are concerned with a notion of ecological function as the contribution of an organism, population, species, or abiotic item to the maintenance of its community and/or the functioning of its ecosystem. Millstein’s arguments hence do not invalidate the consensus view but draw (...) attention to a notion of function that has been neglected in philosophical discussions and that deserves more attention. (shrink)

Dans un monde dominé par les conflits, il arrive qu’il faille se défendre. L’invention des armes a évolué en parallèle avec le savoir technique, puis scientifique, et il est même arrivé que la recherche d’applications militaires ait joué un rôle moteur dans la découverte scientifique. Lorsque les armes ne servent pas à attaquer d’autres nations, leur fabrication et leur commerce se justifient morale- ment. Il faut cependant qu’elles ne puissent échapper à ceux qui les construisent et doivent en contrôler la (...) diffusion. Facilement mise en œuvre, la guerre utilisant des organismes vivants ou ce qu’ils pro- duisent comme armes est très ancienne. Or l’originalité des êtres vivants est qu’ils se multiplient, qu’un seul individu suffit à recouvrir la Terre de ses descendants. La biologie ne se prête jamais à un usage militaire moralement défendable parce que le confinement au champ de bataille est impossible. De ce fait, les applications de la biologie ont été vite écartées du domaine de la Défense permise par les traités internationaux. La Convention de 1972 sur l’Interdiction des Armes Biologiques et à Toxines (CIABT), entrée en vigueur en 1975, est aujourd’hui signée par 183 pays (ratifiée par 175) sur un total de 193, sans compter Taïwan qui l’a ratifiée mais n’est pas reconnu par l’ONU. Elle interdit la mise au point, la fabrication, l’acquisition, le transfert, la conservation, le stockage et l’utilisation des armes bio- logiques et à toxines. Elle constitue un élément essentiel de la lutte contre la prolifération des armes de destruction massive. (shrink)

It is widely agreed that fiction is necessarily incomplete, but some recent work postulates the existence of universal fictions—stories according to which everything is true. Building such a story is supposedly straightforward: authors can either assert that everything is true in their story, define a complement function that does the assertoric work for them, or, most compellingly, write a story combining a contradiction with the principle of explosion. The case for universal fictions thus turns on the intuitive priority we assign (...) to the law of non-contradiction. My goal in this paper is to show that our critical and reflective literary practices set constraints on story-telling which preclude universal fictions. I will raise four stumbling blocks for universal fictionalists: the gap between saying and making true, our actual interpretive reactions to story-level contradictions, the criteria we accept for what counts as a story in our literary practices, and the undesirability of the universal fictionalist’s closure principles. (shrink)

This paper criticizes Jerome Wakefield’s harmful dysfunction analysis of disorder by arguing that the conceptual linkage it establishes between the medical concepts of health and disorder and the prudential notions of well-being and harm makes the account inapplicable to nonsentient organisms, such as plants, fungi, and many invertebrate animals. Drawing on a previous formulation of this criticism by Christopher Boorse, and noting that Wakefield could avoid it if he adopted a partly biofunction-based account of interests like that often advocated in (...) the field of environmental ethics, I argue that integrating such an account of interests into the HDA would generate serious concerns. Specifically, it would make dysfunction sufficient for disorder and so reestablish between dysfunction and disorder precisely the kind of sufficiency relation that harm-requiring accounts of disorder strive to avoid; blur the line between the HDA’s dysfunction and harm components and, in so doing, deprive the HDA of its alleged main advantage over monistic dysfunction-based accounts of disorders like Boorse’s; and tie the HDA to an understanding of harm that is in itself problematic. I argue that these three concerns, and the dilemmas they generate, rob the HDA of much of its prima facie appeal, ultimately indicating that a satisfactory account of disorder should most likely eschew all references to prudential notions of well-being and harm. (shrink)

Synthetic biology (SynBio) covers two main areas: application engineering, exemplified by metabolic engi- neering, and the design of life from artificial building blocks. As the general public is often reluctant to embrace synthetic approaches, preferring nature to artifice, its immediate future will depend very much on the public’s reaction to the unmet needs created by the pervasive demands of sustainability. On the other hand, this reluctance should not have a negative impact on research that will now take into account the (...) existence of the multiple transitions that cells face over time. The ages of life—birth, development, maturation, senescence and death—reflect specific key transitions and have, until now, rarely been taken into account in SynBio designs. This results in a mismatch between novelty and the very long evolutionary time that led to the existing chassis [remember that this is the common term used to describe the cellular framework as seen by synthetic biologists (de Lorenzo & Danchin, 2008)]. It also implies that, in general, transitions between growth stages will be taken into account with the appro- priate embodiment of highly specific processes. This is particularly important when adapting new models to their host, whether natural or artificial. Adaptation fol- lows two stages, short-term accommodation of new entities and long-term assimilation into the cell as a whole. This requires discrimination between classes of entities. We suggest that proteins playing the essential role of Maxwell’ demons, here named Maxwell’s dis- criminators (MxDs) to refer to their original function, will permit the assimilation and accommodation of artificial constructs. As a consequence, we can foresee that class discrimination, beyond mere recognition, will be implemented in SynBio 2.0, leading to an authentic par- adigm shift (Kuhn, 1996), based on conceptions that embody information as a genuine currency of reality. (shrink)

Francis Sparshott introduced the term ‘remote art’ in his 1982 presidential address to the American Society for Aesthetics. The concept has not drawn much notice since—although individual remote arts, such as palaeolithic art and the artistic practices of subaltern cultures, have enjoyed their fair share of attention from aestheticians. This paper explores what unites some artistic practices under the banner of remote art, arguing that remoteness is primarily a matter of some audience’s epistemic distance from a work’s context of creation. (...) I introduce palaeoart—the depiction of extinct prehistoric fauna and flora, especially from the Mesozoic—as a paradigmatic case of remote art, showing that its remoteness is secured both by the deceptively rich cognitive load required for its creation and appreciation, and by its existence at the margins of the institutional artworld, which ensures that this cognitive loading is largely obscured. Too often, remote art is not just inscrutable, it is invisible to us. (shrink)

Assembly of minimal genomes revealed many genes encoding unknown functions. Three overlooked functional categories account for some of them. Cells are prone to make errors and age. As a first key function, discrimination between proper and changed entities is indispensable. Discrimination requires management of information, an authentic, yet abstract, cur- rency of reality. For example proteins age, sometimes very fast. The cell must identify, then get rid of old proteins without destroying young ones. Implementing discrimination in cells leads to the (...) second set of functions, usually ignored. Being abstract, information must nevertheless be embodied into material entities, with unavoidable idiosyncratic properties. This brings about novel unmet needs. Hence, the buildup of cells elicits specific but awkward material implementations, ‘kludges’ that become essential under particular settings, while difficult to identify. Finally, a third functional category char- acterizes the need for growth, with metabolic implementations allowing the cell to put together the growth of its cytoplasm, membranes, and genome, spanning different spatial dimensions. Solving this metabolic quandary, critical for engineering novel synthetic biology chassis, uncovered an unexpected role for CTP synthetase as the coordinator of nonhomothetic growth. Because a significant number of SynBio constructs aim at creating cell factories we expect that they will be attacked by viruses (it is not by chance that the function of the CRISPR system was identified in industrial settings). Substantiating the role of CTP, natural selection has dealt with this hurdle via synthesis of the antimetabolite 30-deoxy-30,40-didehydro- CTP, recruited for antiviral immunity in all domains of life. (shrink)

The lasting effects of the debate over canon-formation during the 1980s affected the whole field of Humanities, which became increasingly engaged in interrogating the origin and function of the Western canon. In philosophy, a great deal of criticism was, as a result, directed at the traditional narrative of seventeenth-and eighteenth-century philosophies—a critique informed by postcolonialism as well as feminist historiography. D. F. Norton, L. Loeb and many others1 attempted to demonstrate the weaknesses of the tripartite division between rationalism, empiricism and (...) critical philosophy.2 As time went on, symptoms of dissatisfaction with what has... (shrink)

The emergence of new techniques in both microbial biotechnology and artificial intelligence (AI) is opening up a completely new field for monitoring and sometimes even controlling the evolution of pathogens. However, the now famous generative AI extracts and reorganizes prior knowledge from large datasets, making it poorly suited to making predictions in an unreliable future. In contrast, an unfamiliar perspective can help us identify key issues related to the emergence of new technologies, such as those arising from synthetic biology, whilst (...) revisiting old views of AI or including generative AI as a generator of abduction as a resource. This could enable us to identify dangerous situations that are bound to emerge in the not-too-distant future, and prepare ourselves to anticipate when and where they will occur. Here, we emphasize the fact that amongst the many causes of pathogen outbreaks, often driven by the explosion of the human population, laboratory accidents are a major cause of epidemics. This review, limited to animal pathogens, concludes with a discussion of potential epidemic origins based on unusual organisms or associations of organisms that have rarely been highlighted or studied. (shrink)

Margulis’ evolutionary theory entails a revision of certain core concepts of traditional biology. One of these changes is related to the hot debate about units of selection. This paper considers Margulis’ proposal as a new research tradition (RT) and evaluates its consequences to the mentioned issue. Three ideas are suggested here: firstly, that her theory represents the revision of many classical biological concepts; secondly, that her position implies a reappraisal of many traditional issues in philosophy of biology; and thirdly, that (...) studying it from Lakatos and Laudan’s ideas about RT allows us to enlighten the richness of her theory. (shrink)

This article offers an analysis of ecologist Charles Elton’s “functional” concept of the niche and of the notion of function implicitly associated with it. It does so in part by situating Elton’s niche concept within the broader context of the “functionalist-interactionist” approach to ecology he introduced, and in relation to his views on the relationship between ecology and evolution. This involves criticizing the common claim that Elton’s idea of species as fulfilling functional roles within ecological communities committed him to an (...) idea of communities as units of selection. While such a claim implicitly attributes to Elton an understanding of function along the lines of the selected-effects theory of function advocated by many biologists and philosophers of biology, Elton’s use of the niche concept, I maintain, involves an understanding of function more along the lines of alternative nonselectionist theories such as the causal-role, goal-contribution, and organizational theories. I also briefly discuss how ecologists after Elton also tend to have typically adopted a nonselectionist understanding of the function concept, similar to his. (shrink)

Science and engineering rely on the accumulation and dissemination of knowledge to make discoveries and create new designs. Discovery-driven genome research rests on knowledge passed on via gene annotations. In response to the deluge of sequencing big data, standard annotation practice employs automated procedures that rely on majority rules. We argue this hinders progress through the generation and propagation of errors, leading investigators into blind alleys. More subtly, this inductive process discourages the discovery of novelty, which remains essential in biological (...) research and reflects the nature of biology itself. Annotation systems, rather than being repositories of facts, should be tools that support multiple modes of inference. By combining deduction, induction and abduction, investigators can generate hypotheses when accurate knowledge is extracted from model databases. A key stance is to depart from ‘the sequence tells the structure tells the function’ fallacy, placing function first. We illustrate our approach with examples of critical or unexpected pathways, using MicroScope to demonstrate how tools can be implemented following the principles we advocate. We end with a challenge to the reader. (shrink)

Although Boorse’s and Wakefield’s accounts of health are generally regarded as competing ones, they are in fact so only if they are aimed at the same concept. Some remarks made by Boorse and Wakefield, however, leave it unclear whether they are. On one possible interpretation, Boorse’s account aims at analysing a theoreticalconcept of abnormality, which ought to be distinguished from a more clinicalor therapeuticconcept, whereas Wakefield’s account aims at analysing a clinicalor therapeuticconcept. The debate between Boorse and Wakefield would then (...) either be merely terminological, or would boil down to whether Boorse is correct to assert the existence of a theoreticalconcept of abnormality which ought to be distinguished from a clinicalor therapeuticone. This paper aims to clarify what is at stake between Boorse and Wakefield, by maintaining that their accounts are most plausibly interpreted as both being aimed towards a theoreticalconcept of abnormality. (shrink)

This paper reinforces the current consensus against the applicability of the selected effect theory of function in ecology. It does so by presenting an argument which, in contrast with the usual argument invoked in support of this consensus, is not based on claims about whether ecosystems are customary units of natural selection. Instead, the argument developed here is based on observations about the use of the function concept in functional ecology, and more specifically, research into the relationship between biodiversity and (...) ecosystem functioning. It is argued that a selected effect account of ecological functions is made implausible by the fact that it would conflict with important aspects of the understanding of function and ecosystem functional organization which underpins functional ecology’s research program. Specifically, it would conflict with (1) Functional ecology’s adoption of a context-based understanding of function and its aim to study the functional equivalence between phylogenetically-divergent organisms; (2) Functional ecology’s attribution to ecosystems of a lower degree of part-whole integration than the one found in paradigm individual organisms; and (3) Functional ecology’s adoption of a physiological or metabolic perspective on ecosystems rather than an evolutionary one. (shrink)

Although an advantage commonly claimed for selected effects theories of function lies in their ability to eschew a problem of liberality that alternative theories allegedly face, they also face their own liberality problem. This problem is classically illustrated by Mark Bedau’s case of clay crystals, which seem apt to undergo a kind of natural selection, and also, more recently, by Justine Kingsbury’s example of rocks differentially persisting on a beach, discussed by Justin Garson in relation to his generalized selected effects (...) theory. In this paper, I will be concerned with another type of case that illustrates this liberality problem: whole organisms. Although we may be reluctant to consider whole organisms as potential function bearers, they seem uncontestably subject to a selection process (i.e. natural selection), such that selected effects theories seem prima facie committed to ascribing them functions. I will use the case of whole organisms to comparatively assess two influential responses to the liberality problem faced by selected effects theories: the service response, which introduces the requirement that selected effects functions result from selection for a contribution to a complexly organized system, and the population response, which restricts selected effects functions to effects that result from selection processes operating on populations of the appropriate type. I will argue that, although the latter response has been preferred in Garson and others’ recent discussions of selected effects theories, the case of whole organisms shows the superiority of the former. Selected effects functions arise not from selection simpliciter, but from selection for service. (shrink)

This paper introduces the reconstitutor as a comprehensive unit of heredity within the context of evolutionary research. A reconstitutor is the structure resulting from a set of relationships between different elements or processes that are actively involved in the recreation of a specific phenotypic variant in each generation regardless of the biomolecular basis of the elements or whether they stand in a continuous line of ancestry. Firstly, we justify the necessity of introducing the reconstitutor by showing the limitations of other (...) evolutionary conceptions of the unit of heredity, such as the replicator, the reproducer, and the Darwinian individual. We argue that these conceptions are based on the requirement of lineage formation, which we argue to be unnecessary for the existence of evolutionary heredity. In the second part, we introduce the reconstitutor, which we base on the concept of Stability of Traits, and illustrate how it covers cases of hereditary phenomena not covered by the previous accounts. Secondly, we illustrate how the reconstitutor could serve as a platform to rethink ecological inheritance and other forms of inheritance that have been recently introduced under the song/singer model of evolution. (shrink)

Synthetic biology aims at reconstructing life to put to the test the limits of our understanding. It is based on premises similar to those which permitted invention of computers, where a machine, which reproduces over time, runs a program, which replicates. The underlying heuristics explored here is that an authentic category of reality, information, must be coupled with the standard categories, matter, energy, space and time to account for what life is. The use of this still elusive category permits us (...) to interact with reality via construction of self-consistent models producing predictions which can be instantiated into experiments. While the present theory of information has much to say about the program, with the creative properties of recursivity at its heart, we almost entirely lack a theory of the information supporting the machine. We suggest that the program of life codes for processes meant to trap information which comes from the context provided by the environment of the machine. (shrink)

This paper analyzes community ecologist Charles Elton’s ideas on animal communities, and situates them with respect to the classical opposition between organicist–holistic and individualistic–reductionist ecological views drawn by many historians of ecology. It is argued that Elton espoused a moderate ecological holism, which drew a middle way between the stricter ecological holism advocated by organicist ecologists and the merely aggregationist views advocated by some of their opponents. It is also argued that Elton’s moderate ecological holism resonated with his preference for (...) analogies between ecological communities and human societies over more common ones between communities and individual organisms. I discuss, on the one hand, how the functionalist-interactionist approach to community ecology introduced by Elton entailed a view of ecological communities as more or less self-maintaining functionally organized wholes, and how his ideas on this matter were incorporated into their views by organicist ecologists Frederic Clements, Victor Shelford, and Warder C. Allee et al. On the other hand, I identify some important divergences between Elton’s ecological ideas and those of organicist ecologists. Specifically, I show how Elton’s ideas on species distribution, animal migrations, and ecological succession entailed a view of animal communities as exhibiting a weaker degree of part-whole integration than that attributed to them by Clements and Shelford; and how Elton’s mixed stance on the balance of nature idea and his associated views on community stability attributed to communities a weaker form of self-regulation than that attributed to them by Allee et al. (shrink)

Van Rensselaer Potter (1911-2001), le biologiste à l’origine du terme « bioéthique » dans les écrits nord-américains, considère que « real bioethics falls in the context of the ideals of […] Aldo Leopold », un forestier, philosophe et poète ayant marqué le XXe siècle. Associer Leopold à Potter a pour effet de placer la bioéthique dans la famille des éthiques de l’environnement, ce qui la différencie du sens conventionnel retenu en médecine et en recherche depuis le Rapport Belmont (1979), une (...) déclaration ayant propulsé l’institutionnalisation de la bioéthique en Amérique du Nord. Cependant, diviser la bioéthique entre le médical et l’environnemental est réducteur. Potter propose au contraire une bioéthique globale s’intéressant aux enjeux situés à leur interface, dont ceux concernant la terre, la vie sauvage, la surpopulation, la consommation, etc. Cet article vise à amorcer un nouveau chantier d’analyse de la pensée de Potter en s’appuyant sur l’héritage de Leopold en biologie. Une synthèse de cette vision potterienne est proposée de manière à considérer son œuvre comme un tout cohérent s’intégrant aux grands débats qui transcendent les XXe et XXIe siècles. Sa vision apparaît comme une sagesse collective et prospective sous la forme d’une science de la survie et d’un code de bioéthique. Dépassant l’éthique de l’environnement, son association avec Leopold offre un modèle de la complexité s’imposant comme cas indissociable du contexte qui l’englobe, en améliorant nos façons d’intervenir en pratique dans un monde en constante transformation, à titre de gouvernance adaptative et de sagesse de la responsabilité. (shrink)

The writings by the 'state philosophers' of nineteenth-century France are often seen, either as entirely driven by political or ideological concerns, or reduced to mere history of philosophy. Hence, ironically, those who established the philosophical canon that still now informs philosophy teaching in France were themselves excluded from that canon. Using the heuristic concept of a philosophical figure, this contribution intends to show how, for these philosophers, historiography represented a seemingly inoffensive, but in reality extremely efficient, means of searching out (...) philosophical alternatives to the institutionally dominant philosophy of Victor Cousin (1792-1867). Focalizing on the almost forgotten case of Joseph-Marie Degérando (1772-1842), I show how he used the philosophical figure of Descartes and how he used it to counter Cousin. (shrink)

Science is founded on a method based on critical thinking. A prerequisite for this is not only a sufficient command of language but also the comprehension of the basic concepts underlying our understanding of reality. This constraint implies an awareness of the fact that the truth of the World is not directly accessible to us, but can only be glimpsed through the construction of mod- els designed to anticipate its behaviour. Because the relationship between models and reality rests on the (...) interpretation of founding postulates and in- stantiations of their predictions (and is therefore deeply rooted in language and culture), there can be no demarcation between science and non-science. However, critical thinking is essential to ensure that the link between models and reality is gradually made more adequate to reality, based on what has already been established, thus guaranteeing that science progresses on this basis and excluding any form of relativism. (shrink)

Schopenhauer’s invective is legendary among philosophers, and is unmatched in the historical canon. But these complaints are themselves worthy of careful consideration: they are rooted in Schopenhauer’s philosophy of language, which itself reflects the structure of his metaphysics. This short chapter argues that Schopenhauer’s vitriol rewards philosophical attention; not because it expresses his critical take on Fichte, Hegel, Herbart, Schelling, and Schleiermacher, but because it neatly illustrates his philosophy of language. Schopenhauer’s epithets are not merely spiteful slurs; instead, they reflect (...) deep-seated theoretical and methodological commitments to transparency of exposition. (shrink)

In a series of papers, J. Baird Callicott criticizes the wilderness concept of nature and the associated approach to environmentalism which focuses on the preservation of areas of land free of human intervention. As he notes, this concept rests on a human/nature dualism which defines the natural in opposition to the cultural and the artefactual, and thus in principle places humans outside the natural realm. This makes it conceptually impossible for humans to intervene in nature without denaturing it. Callicott rejects (...) this concept of naturalness for two general kinds of reasons. First, because it is socio-politically oppressive, as it is frequently applied to areas where some aboriginal... (shrink)

Anticiper les épidémies est le souhait le plus vif de toutes les institutions qui veillent sur la santé publique. Un raisonnement naïf permet de penser qu’il suffit de faire évoluer en laboratoire un organisme potentiellement pathogène pour savoir comment sa descendance pourra devenir plus virulente pour l’homme. Il est alors facile de faire croître cet organisme sur des cellules humaines, qu’il infecte mal pour commencer, puis de retenir ses descendants au fur et à mesure qu’ils deviennent plus infectieux. La vision (...) optimiste affirme alors que les caractériser permettra de construire des défenses appropriées. Bien des variations sur ce thème sont possibles, y compris avec l’aide de la synthèse artificielle de variants dont on saurait imaginer la pathogénicité pour l’homme. Depuis plus de deux décennies, des chercheurs développent des expériences de ce type, dite de « gain de fonction » (GdF). Leur interprétation repose sur l’illusion que nous savons prévoir l’évolution des êtres vivants. En réalité, ceux que nous observons aujourd’hui ont été sélectionnés au cours du temps précisément parce qu’ils conduisent toujours à des comportements imprévisibles. Une règle clé de l’évolution est que la vie, pour durer dans des circonstances qui ne peuvent être prévues, doit sans cesse faire émerger des formes innovantes. À ce caractère propre à la vie s’ajoute un imprévisible lié à l’impéritie humaine, cause de l’omniprésence des accidents de laboratoire. Or, en virologie spécialement, l’accident est la règle et non l’exception. Il faut ajouter que le caractère public de ces expériences les rend utilisables par toutes les structures malveillantes qui sont hélas répandues dans le monde. Il n’est pas difficile alors d’imaginer les conséquences catastrophiques des expériences de GdF. Nous proposons donc qu’elles soient purement et simplement interdites et que toute transgression soit sévèrement punie, en frappant d’abord au porte-monnaie, ce qui semble être la meilleure façon de faire dans nos sociétés devenues universellement vénales. (shrink)

The abstract basis of modern computation is the formal description of a finite state machine, the Universal Turing Machine, based on manipulation of integers and logic symbols. In this contribution to the discourse on the computer-brain analogy, we discuss the extent to which analog computing, as performed by the mammalian brain, is like and unlike the digital computing of Universal Turing Machines. We begin with ordinary reality being a permanent dialog between continuous and discontinuous worlds. So it is with computing, (...) which can be analog or digital, and is often mixed. The theory behind computers is essentially digital, but efficient simulations of phenomena can be performed by analog devices; indeed, any physical calculation requires implementation in the physical world and is therefore analog to some extent, despite being based on abstract logic and arithmetic. The mammalian brain, comprised of neuronal networks, functions as an analog device and has given rise to artificial neural networks that are implemented as digital algorithms but function as analog models would. Analog constructs compute with the implementation of a variety of feedback and feedforward loops. In contrast, digital algorithms allow the implementation of recursive processes that enable them to generate unparalleled emergent properties. We briefly illustrate how the cortical organization of neurons can integrate signals and make predictions analogically. While we conclude that brains are not digital computers, we speculate on the recent implementation of human writing in the brain as a possible digital path that slowly evolves the brain into a genuine (slow) Turing machine. (shrink)

Pasteur’s originality in the way he developed pure research is to have understood the importance, for society, of the underlying motivation. Curiosity, of course, is a strong motivation, which explains why we seek to understand the origin of life. But, in front of the immensity of the possible choices, why not, also, choose to start from questions of economic interest (diseases of beer and wine, diseases aVecting the silk industry . . . ) Finally, of course, health is a constant (...) preoccupation, but the diseases, which have no borders, often come from tropical countries and Asia especially. It is therefore necessary to settle there, but not to come and impose one’s point of view, but on the contrary to use the knowledge coming from the local culture in order to open new ways of understanding the reality of the world. (shrink)

In this paper we analyze Libet’s conclusions on «free will» (FW), rejecting his view of the concept and defending a partially aligned view with Wittgenstein’s early remarks on FW. First, the concept of Readiness Potential (RP) and Libet’s view are presented. Second, we offer an account of Wittgenstein´s point of view. Third, a dual-domain analysis is proposed; finally, we offer our conclusions. This article´s conclusions are part of an ongoing research.

Les études dites de réception se trouvent aujourd’hui dans une situation paradoxale. Au premier regard le tableau paraît souriant. Anciens ou modernes, les textes sont aujourd’hui communément abordés sous l’angle de leurs lectures immédiates (réception médiatique notamment) et, surtout, de leurs aménagements posthumes (avatars éditoriaux, propositions herméneutiques, usages sociaux). La multiplication de pareils travaux manifeste un engouement qui ne semble pas près de se démentir. Spectaculaire si l’on considère le nombre de thèses et de colloques qui entretiennent cette vague, pareil (...) essor ne suffit pourtant pas à lever tous les doutes. Loin de faire l’unanimité, les études dites de réception suscitent toujours une certaine méfiance. Ne seraient-elles pas le Cheval de Troie d’un relativisme conduisant à niveler toutes les formes de critiques et d’interprétations? Outre la crainte d’une dangereuse indifférenciation, un soupçon plus radical remet en cause leur bien-fondé : s’intéresser à l’histoire des gestes critiques et des modes de lecture, n’est-ce pas un indice d’épuisement pour des champs disciplinaires n’ayant d’autre objet que leur propre histoire? Ce dossier fait le pari inverse. Il doit son impulsion à la conviction qu’un regard patient et informé sur les actes de lecture de nos prédécesseurs éclaire, en retour, nos propres pratiques. Accuser réception : ce titre voudrait suggérer, par-delà les procès en illégitimité, la nécessité de prendre en compte la vie longue des textes pour mieux comprendre ce que nous faisons quand, après tant d’autres et parfois dans leur ombre, nous lisons les textes du passé. Rassemblant les contributions de spécialistes venus d’horizons divers comme l’histoire de la philosophie occidentale, celles de la poésie chinoise, des littératures médiévales et modernes ou encore de l’herméneutique biblique, ce dossier, qui mêle études monographiques et réflexions transversales, analyse la constitution de certains paradigmes critiques, mais également celle de territoires disciplinaires fondés sur des traditions interprétatives parfois oubliées. Il espère montrer que la question des réceptions n’est pas réductible à la somme figée des commentaires formulés sur un texte, un auteur ou une période. Posée de manière dynamique, elle donne à voir la production des héritages qui nous ont été transmis et permet ainsi d’arpenter autrement les paysages qui sont devenus les nôtres. Textes réunis par Stéphane Zékian et Thierry Roger et mis en ligne avec le soutien de l'Université de Lausanne. (shrink)

Christopher Boorse’s Biostatistical Theory of Health has been the main contender among naturalistic accounts of health for the last 40 years. Yet, a recent criticism of this theory, presented by Elselijn Kingma, identifies a dilemma resulting from the BST’s conceptual linking of health and statistical typicality. Kingma argues that the BST either cannot accommodate the situation- specificity of many normal functions or cannot account for many situation-specific diseases. In this article, we expand upon with Daniel Hausman’s response to Kingma’s dilemma. (...) We propose that recalling Boorse’s specification that health is an intrinsic property of its bearers and explicating this intrinsic property in relation to the concept of homeostasis can illuminate how proponents of naturalistic accounts of health should deal with the situation- specificity of normal functions. We argue that beyond what Boorse and Hausman have delineated, the situation- specificity of normal function cannot be fully captured in a simple dichotomy between normal and abnormal environment or between relevant and irrelevant situations. By bringing homeostasis to the fore of the analysis of health, we set out a richer picture of what the various situations that affect living organisms’ functional performance can be. Accordingly, we provide a broader classification of these various situations which, we contend, better accounts for the main intuitions that philosophers of medicine have sought to accommodate than previous naturalistic theories of health. (shrink)

The notion of antifragility, an attribute of systems that makes them thrive under variable conditions, has recently been proposed by Nassim Taleb in a business context. This idea requires the ability of such systems to ‘tinker’, i.e., to creatively respond to changes in their environment. A fairly obvious example of this is natural selection-driven evolution. In this ubiquitous process, an original entity, challenged by an ever-changing environment, creates variants that evolve into novel entities. Analyzing functions that are essential during stationary-state (...) life yield examples of entities that may be antifragile. One such example is proteins with flexible regions that can undergo functional alteration of their side residues or backbone and thus implement the tinkering that leads to antifragility. This in-built property of the cell chassis must be taken into account when considering construction of cell factories driven by engineering principles. (shrink)

This article is part of a For-Discussion-Section of Methods of Information in Medicine about the paper "Biomedical Informatics: We Are What We Publish", written by Peter L. Elkin, Steven H. Brown, and Graham Wright. It is introduced by an editorial. This article contains the combined commentaries invited to independently comment on the Elkin et al. paper. In subsequent issues the discussion can continue through letters to the editor.

It is often thought that the boundaries and properties of art-kinds are determined by the things we say and think about them. More recently, this tendency has manifested itself as concept-descriptivism, the view that the reference of art-kind terms is fixed by the ontological properties explicitly or implicitly ascribed to art and art-kinds by competent users of those terms. Competent users are therefore immune from radical error in their ascriptions; the result is that the ontology of art must begin and (...) end with conceptual analysis. Against this tendency towards concept-driven ontology, I offer a trio of objections derived from: the cultural and temporal variability of concepts of art, the systematic tendency, on the part of would-be ontological assessors, to err on the side of familiar categories or, conversely, to exaggerate minor differences between familiar and unfamiliar practices, and the influence artworld precedents exert over expert and folk concepts alike. These considerations, I argue, mandate an epistemic humility that is simply unavailable to the concept-descriptivist. (shrink)

The place given by Cousin to Condillac in the project of founding a new “French Philosophy” in the first half of 19th century France seems eminently paradoxical. On the one hand, Condillac is designated as one of the main representatives of this specifically 18th century sensualism that has to be fought by all means. But on the other hand, Cousin recognises that in Condillac “the metaphysician dominates”. What is more, he does not hesitate to present Condillac as “the only, the (...) true French metaphysician of the 18th century”. This Condillac is thus likely to constitute a positive reference. Shedding of light on a very little known intertextuality between Cousin, Saphary and Degérando, this chapter attests to the crucial importance of the identification of the true philosophical lineage between the new French and spiritualist school and Condillac in the first decades of the 19th century. The paradoxical dimension of Condillac’s philosophy thus appears to be found in the empirical nature and the eminently practical vocation of this metaphysics, which must enable the founding of a new psychology, other morals and other politics. Which is a great leverage to shatter the philosophical dualisms and antagonisms structuring the official historiography of modernity we mainly inherit from 19th century France. Empiricism, French Philosophy, Historiography, Metaphysics, Reception Studies, Sensualism, Spiritualism. (shrink)

The dichotomy between the research to generate knowledge and the application of that knowledge to benefit mankind seems to be a recent development. In fact, more than 100 years ago Louis Pasteur avoided this debate altogether: one of his major, yet forgotten, contributions to science was the insight that research and its applications are not opposed, but orthogonal to each other (Stokes, 1997). If Niels Bohr ‘invented’ basic academic research—which was nevertheless the basis for many technological inventions and industrial applications—Pasteur (...) developed what we might call ‘motivated’ research. -/- How is research motivated and by what? By definition, scientists are citizens and members of the general public and, like the public, they are motivated by two forces: on the one hand, in Rudyard Kipling's words, “man's insatiable curiosity”; on the other hand, a desire for maintaining and improving their well‐being. These are not contradictory to one another; curiosity nourishes dreams of a brighter future and leads to discoveries that contribute to well‐being. (shrink)

It has recently been argued that metal’s ‘heaviness’ is conceptually inarticulable. I argue, on the contrary, that ‘heaviness’ is a matter of inaccessibility—the ‘something more’ that makes metal ‘heavy’ is actually something less: less auditory processing fluency. Like profound literature, metal resists, but also invites and rewards, interpretation. I argue that understanding ‘heaviness’ in terms of auditory processing fluency allows us to make sense of a number of otherwise puzzling features of the music, and to articulate a unifying gestalt for (...) the genre. (shrink)