This paper will begin with some very broad and general considerations about the kind of biological entities we are. This exercise is motivated by the belief that the view of what we—multicellular eukaryotic organisms—are that is widely assumed by biologists, medical scientists and the general public, is an extremely limited one. It cannot be assumed a priori that a more sophisticated view will make a major difference to the science or practice of medicine, and there are areas of (...) medicine to which it is probably largely irrelevant. However, in this case there are important implications for medicine, or so I shall argue. In particular, it enables us to appreciate fully the potential medical significance of some of the most exciting contemporary advances in general biology, in such fields as epigenetics, metagenomics, and systems biology; and part of this significance is that these advances have raised serious doubts about how we should understand the biological individuals that medicine is generally assumed to aim to treat. (shrink)

Contemporary biology has inherited two key assumptions from the Modern Synthesis about the nature of population lineages: sexual reproduction is the exemplar for how individuals in population lineages inherit traits from their parents, and random mating is the exemplar for reproductive interaction. While these assumptions have been extremely fruitful for a number of fields, such as population genetics and phylogenetics, they are increasingly unviable for studying the full diversity and evolution of life. I introduce the “mixture” account of population lineages (...) that escapes these assumptions by dissolving the Modern Synthesis’s sharp line separating reproduction and development and characterizing reproductive integration in population lineages by the ephemerality of isolated subgroups rather than random mating. The mixture account provides a single criterion for reproductive integration that accommodates both sexual and asexual reproduction, unifying their treatment under Kevin de Queiroz’s generalized lineage concept of species. The account also provides a new basis for empirically assessing the effect of random mating as an idealization on the empirical adequacy of population genetic models. (shrink)

The relation between method, concept and theory in science is complicated. I seek to shed light on that relation by considering an instance of it in systematics: The additional challenges phylogeneticists face when reconstructing phylogeny not at a single level, but simultaneously at multiple levels of the hierarchy. How does this complicate the task of phylogenetic inference, and how might it inform and shape the conceptual foundations of phylogenetics? This offers a lens through which the interplay of method, theory (...) and concepts may be understood in systematics, which, in turn, provides data for a more general account. (shrink)

Biology lacks a central organism concept that unambiguously marks the distinction between organism and non-organism because the most important questions about organisms do not depend on this concept. I argue that the two main ways to discover useful biological generalizations about multicellular organization--the study of homology within multicellular lineages and of convergent evolution across lineages in which multicellularity has been independently established--do not require what would have to be a stipulative sharpening of an organism concept.

Le général André Bach dans une réflexion sur l’« horizon de mort dans la violence de guerre » part d’une approche anthropologique du phénomène de violence et de la peur (quasiment biologique) qu’il engendre en soulignant les difficultés des sociétés occidentales à penser la mort. C’est l’État qui donne à la guerre un sens politique et sacré et qui crée les catégories fonctionnelles de la guerre (les concepts de paix et de guerre ne sont pas en eux-mêmes opérationnels). Dans le (...) cadre d’une réflexion clausewitzienne sur la montée aux extrêmes, l’« extrême » pour le soldat est toujours sa propre mort (plus que celle de l’ennemi). Les notions de barbarisation et humanisation ne peuvent en ce sens rendre compte de la violence et de la peur radicales présentes dans toute guerre où le rôle du commandement est toujours de mettre en œuvre un degré de violence supérieur à celui de l’adversaire, sans aucune considération de « proportionnalité » de cette violence. La mise à distance technique ne diminue pas la violence mais l’augmente à proportion de l’éloignement de la peur. Seul le politique peut et doit mettre des limites à cette violence militaire par nature illimitée. La modernisation des armes ne relève jamais d’une humanisation du combat mais d’une recherche d’une violence plus efficace. L’entraînement du soldat en temps de paix n’est jamais entraînement à la violence mais apprentissage de savoir-faire et effort de constitution d’un groupe soudé, doté d’un bon moral. L’ordre et la formation tentent de limiter la sauvagerie mais il existe une constitution endogène de comportements propres au soldat, que la hiérarchie tente de canaliser dans une symbolique guerrière fondée sur le sentiment de l’honneur (destiné à compenser la peur d’être une proie vouée à mourir et à faire préférer la lutte au coude à coude sur l’instinct de conservation). Le couple violence/honneur fait que l’armée dépourvue de contrat social n’est pas soluble dans le politique (aujourd’hui dans les écoles militaires on ne parle plus d’« honneur » mais d’« éthique »…, mais pour dire la même chose). La conscription fut une rupture de la logique endogène de l’armée et introduisit une brèche dans ce système archaïque. Mais religion (au Moyen Âge) ou logique démocratique (de nos jours) s’avèrent surtout des « béquilles idéologiques » qui, en définitive, sont souvent plus efficaces pour accroître la barbarisation que pour l’éviter (exemple de la colonisation algérienne où une armée de paix, fonctionnarisée et rigoureusement canalisée, appartenant à une génération n’ayant jamais connu de violence de guerre, développe des massacres de masse). (shrink)

Biology lacks a central organism concept that unambiguously marks the distinction between organism and non-organism because the most important questions about organisms do not depend on this concept. I argue that the two main ways to discover useful biological generalizations about multicellular organization—the study of homology within multicellular lineages and of convergent evolution across lineages in which multicellularity has been independently established—do not require what would have to be a stipulative sharpening of an organism concept.

Species concepts for bacteria and other microbes are contentious, because they are often asexual. There is a Problem of Homogeneity: every mutation in an asexual lineage forms a new strain, of which all descendents are clones until a new mutation occurs. We should expect that asexual organisms would form a smear or continuum. What causes the internal homogeneity of asexual lineages, if they are in fact homogeneous? Is there a natural “species concept” for “microbes”? Two main concepts devised (...) for metazoans and metaphytes have been applied to bacteria. One is the Recombination Concept, a revised form of the Biological Species Concept in which the homogenizing mechanism is the sharing of genome fragments, somewhat akin to sexual recombination. The other is the Ecological Species Concept, in which the ecological niche is that which maintains lineages as cohesive. In this paper I will discuss these two concepts, and offer an underlying model that conjoins them, and consider the implications for species concepts in general. In short, my argument is that asexual species are instances of the most primitive and underived notion of species, which I will call “quasispecies”, following Eigen, and that sexual species are merely one derived kind of species. Moreover, I will argue that there is a continuum of recombination from simple viral models in which each strain is a clone, through to obligate recombination of 50% of the parents’ genome, and that consequently there is no sharp division between “microbial” and more familiar species. (shrink)

This article challenges the orthodox view that there is and can be no scientifically valid concept of race applicable to human beings by presenting a candidate scientific concept of biological race. The populationist concept of race specifies that a “race” is a subdivision of Homo sapiens—a group of populations that exhibits a distinctive pattern of genetically transmitted phenotypic characters and that belongs to an endogamous biological lineage initiated by a geographically separated and reproductively isolated founding population. (...) The viability of the PRC is shown by demonstrating its capacity to withstand a wide range of objections. A common theme is that the objections turn on misconceptions of the idea of a scientific concept of race. The final section argues that the PRC will not foster racism. (shrink)

Biological racial realism (BRR) continues to be a much-discussed topic, with several recent papers presenting arguments for the plausibility of some type of “biological race.” In this paper, the focus will be on the phylogenetic conceptions of race, which is one of the most promising views of BRR, that define races as lineages of reproductively isolated breeding populations. However, I will argue that phylogenetic conceptions of race fail to prove that races are biologically real. I will develop and defend my (...) argument against the phylogenetic views of race by relying on current research in population genetics, human evolution, and social sciences. Ultimately, I will argue that (i) race is not a biologically legitimate category and (ii) philosophers should direct their resources to understand problems that arise due to racialization, and thereby they should find solutions to those problems. (shrink)

The Qur'an began to descend in the Arabian Peninsula in a period when the traditions of ignorance were dominant. In the period of ignorance, when weak and powerless people were oppressed, excluded, exploited, humiliated and subjected to various oppressions, being right was not enough. It was also necessary to have the power and strength to get his due. In such a period when the strong are generally considered right, the Qur'an considers every individual created by Allah as a valuable being. (...) As a matter of fact, there are many basic principles in the Qur'an that reinforce the feelings of brotherhood among individuals, strengthen the social fabric and increase trust in society. One of these basic principles is to defend the rights of every weak person regardless of the person's lineage, race, gender and status. In this context, in our study, first of all, the analysis of the meaning of the word of poor in the semantics of the Qur’an, the attitude of the Prophet towards poverty and wealth and which one is superior has been briefly touched upon. Then, information is given about the difference between the concepts of faqîr (the poor person), miskîn (the needy person). After dealing with the basic principles necessary for the protection and care of orphans and for them to live a virtuous life, the situation of oppressed slaves and mustad'af people in society is discussed. (shrink)

The longstanding species problem in biology has a history that suggests a solution, and that history is not the received history found in many texts written by biologists or philosophers. The notion of species as the division into subordinate groups of any generic predicate was the staple of logic from Aristotle through the middle ages until quite recently. However, the biological species concept during the same period was at first subtly and then overtly different. Unlike the logic sense, which (...) relied on definitions of the essence of both genus and species, biological species from the time of Epicurus were consistently considered to involve a reproductive element: in short, living species relied not on essential definitions, but on the generative cause, which might not be definable. I term this the generative conception of species: species were the generation by reproduction of form. This undercuts the claim that species before Darwin were essentialist, and divorces the notion of a type from that of essence. In fact, as late as the end of the nineteenth century, logicians explicitly treated biological “species” as a homonym only of logical essentialist species, and permitted considerable deviation from the type or form. At every point, species in logic were thought to be a subset, in effect, of some more general notion. I sketch a history of both philosophical and biological traditions of the species concept, before turning to the current conceptions. These are reconsidered in the light of this history, and in particular Mayr’s changing views are shown to be somewhat Whiggish, historiographically. Of the many touted biological species concepts, only one of which (Mayr’s) is called _the_ Biological Species Concept, none appears to capture all the relevant facts, intuitions, and operational requirements of biology. Cladistic conceptions, however, have much in common with the older philosophical literature, in that the natural group of cladism is the clade, or monophyletic group. After considering the Individuality Thesis, and the metaphysics of species, we see that species are the most particular terminal taxa in a clade, and that they are “defined” in terms of the particular synapomorphies, or evolved characters, that are causally responsible for keeping the lineages that organisms form distinct from one another. In this way, we can remain within the generative conception of species that has been in play for over two millennia, and yet avoid the pitfalls of prior attempts to find a universal conception of species. (shrink)

Ernst Mayr played a central role in the establishment of the general concept of species as metapopulation lineages, and he is the author of one of the most popular of the numerous alternative definitions of the species category. Reconciliation of incompatible species definitions and the development of a unified species concept require rejecting the interpretation of various contingent properties of metapopulation lineages, including intrinsic reproductive isolation in Mayr's definition, as necessary properties of species. On the other hand, (...) the general concept of species as metapopulation lineages advocated by Mayr forms the foundation of this reconciliation, which follows from a corollary of that concept also advocated by Mayr: the proposition that the species is a fundamental category of biological organization. Although the general metapopulation lineage species concept and Mayr's popular species definition are commonly confused under the name "the biological species concept," they are more or less clearly distinguished in Mayr's early writings on the subject. Virtually all modern concepts and definitions of the species category, not only those that require intrinsic reproductive isolation, are to be considered biological according to the criterion proposed by Mayr. Definitions of the species category that identify a particular contingent property of metapopulation lineages (including intrinsic reproductive isolation) as a necessary property of species reduce the number of metapopulation lineages that are to be recognized taxonomically as species, but they cause conflicts among alternative species definitions and compromise the status of the species as a basic category of biological organization. (shrink)

Responding to a call for systematic contributions on the theory of society, the principle aim of this article is to recover and reconstruct the Young-Hegelian core of critical theory’s theory of the dialectical development of society and, on that basis, to project its creative research-based continuation by analysing its largely neglected key concept of possibility. The acknowledgement of the critical theory lineage’s naturalist, realist and especially idealist features leads this reconstruction to ascribe a central role to certain pivotal (...) concepts that deserve special attention – including nature, the construction of society, evolution, immanent–transcendence and the conceptual conditions or cognitive order of society. A side effect of this theoretical exposition is the exposure in the course of the argument of certain weaknesses often visible in the contemporary articulation of the theory of society in both critical theory and general social theory. Conceptual solutions to those deficiencies are simultaneously presented in a form appropriate to critical theory’s modal-based negative explanatory and positive disclosing critique. (shrink)

This paper isolates a hard, long-standing species problem: developing a comprehensive and exacting theory about the constitutive conditions of the species category, one that is accurate for most of the living world, and which vindicates the widespread view that the species category is of more theoretical import than categories such as genus, sub-species, paradivision, and stirp. The paper then uncovers flaws in several views that imply we have either already solved that hard species problem or dissolved it altogether – so-called (...) We Are Done views. In doing so the paper offers new criticisms of the general lineage species concept (GLSC), evolutionary species concept (EvSC), biological species concept (BSC), other similar concepts, Ereshefsky’s eliminative pluralism about the species category, and both Mishler’s pessimism and Wilkins’ phenomenalism about that category. Opposed to We Are Done views, the paper argues for a Revving Up view, on which we are nearly ready to begin the hard species problem in earnest. To help work towards these conclusions, the paper begins with an outline of a new kind of view of species (Barker 2019a), which proposes they are feedback systems of a mathematically specifiable and empirically testable sort. (shrink)

This collection of original essays--by philosophers of biology, biologists, and cognitive scientists--provides a wide range of perspectives on species. Including contributions from David Hull, John Dupre, David Nanney, Kevin de Queiroz, and Kim Sterelny, amongst others, this book has become especially well-known for the three essays it contains on the homeostatic property cluster view of natural kinds, papers by Richard Boyd, Paul Griffiths, and Robert A. Wilson.

Biologists and philosophers that debate the existence of the species category fall into two camps. Some believe that the species category does not exist and the term 'species' should be eliminated from biology. Others believe that with new biological insights or the application of philosophical ideas, we can be confident that the species category exists. This paper offers a different approach to the species problem. We should be skeptical of the species category, but not skeptical of the existence of those (...) taxa biologists call 'species.' And despite skepticism over the species category, there are pragmatic reasons for keeping the word 'species.' This approach to the species problem is not new. Darwin employed a similar strategy to the species problem 150 years ago. (shrink)

Batterman and Rice ([2014]) argue that minimal models possess explanatory power that cannot be captured by what they call ‘common features’ approaches to explanation. Minimal models are explanatory, according to Batterman and Rice, not in virtue of accurately representing relevant features, but in virtue of answering three questions that provide a ‘story about why large classes of features are irrelevant to the explanandum phenomenon’ ([2014], p. 356). In this article, I argue, first, that a method (the renormalization group) they propose (...) to answer the three questions cannot answer them, at least not by itself. Second, I argue that answers to the three questions are unnecessary to account for the explanatoriness of their minimal models. Finally, I argue that a common features account, what I call the ‘generalized ontic conception of explanation’, can capture the explanatoriness of minimal models. (shrink)

Morar et al. argue that justifications for conservation based on assessments of biodiversity are vacuous, because ‘biodiversity’ is a flawed concept. However, their analysis of the concept mistakes how scientific concepts function. The concept ‘biodiversity’ stands up to their criticisms.

In this paper, I provide an explication and defense of Merleau-Ponty’s theory of concept formation. I argue that at the core of this theory is a distinction between concepts proper and the kinds of generalities characteristic of perceptual experience, which I call “pre-conceptual generalities.” According to Merleau-Ponty, concepts are developed through a two-stage process: first, the establishment of such pre-conceptual generalities, and second, the clarification of these generalities into concepts. I provide phenomenological evidence for the existence of pre-conceptual generalities (...) and explain how they can serve to ground concept formation. To motivate Merleau-Ponty’s account, I consider objections raised by Husserl, Cassirer, and Sellars to the classical philosophical account of empirical concept formation, abstraction. I show that Merleau-Ponty’s distinction between concepts and pre-conceptual generalities provides a philosophically viable account of the formation of empirical concepts while avoiding the problems faced by accounts that rely on abstraction. (shrink)

Mutation and lateral transfer are two categories of processes generating genetic diversity in prokaryotic genomes. Their relative importance varies between lineages, yet both are complementary rather than independent, separable evolutionary forces. The replication process inevitably merges together their effects on the genome. We develop the concept of “open lineages” to characterize evolutionary lineages that over time accumulate more changes in their genomes by lateral transfer than by mutation. They contrast with “closed lineages,” in which most of the changes are (...) caused by mutation. Open and closed lineages are interspersed along the branches of any tree of prokaryotes. This patchy distribution conflicts with the basic assumptions of traditional phylogenetic approaches. As a result, a tree representation including both open and closed lineages is a misrepresentation. The evolution of all prokaryotic lineages cannot be studied under a single model unless new phylogenetic approaches that are more pluralistic about lineage evolution are designed. (shrink)

Polysemous concepts with multiple related meanings pervade natural languages, yet some philosophers argue that we should eliminate them to avoid miscommunication and pointless debates in scientific discourse. This paper defends the legitimacy of polysemous concepts in science against this eliminativist challenge. My approach analyses such concepts as patchworks with multiple scale-dependent, technique-involving, domain-specific and property-targeting uses (patches). I demonstrate the generality of my approach by applying it to "hardness" in materials science, "homology" in evolutionary biology, "gold" in chemistry and "cortical (...) column" in neuroscience. Such patchwork concepts are legitimate if the techniques used to apply them produce reliable results, the domains to which they are applied are homogenous, and the properties they refer to are significant to describe, classify or explain the behavior of entities in the extension of the concept. By following these normative constraints, researchers can avoid miscommunication and pointless debates without having to eliminate polysemous patchwork concepts in scientific discourse. (shrink)

Antinomicity is not necessarily dependent on negation; there is a more general conception of antinomicity based on the fundamental idea of opposition. To study this fact is indispensable to show first that truth and falsity are independent of assertion and negation. Then it can be seen that antinomies can be found everywhere, and that some single categories are in intrinsic opposition with themselves while others are opposed to one another in pairs. An antinomic ‘manifesto’ concludes the work.

We outline the rationale and preliminary results of using the State Context Property (SCOP) formalism, originally developed as a generalization of quantum mechanics, to describe the contextual manner in which concepts are evoked, used, and combined to generate meaning. The quantum formalism was developed to cope with problems arising in the description of (1) the measurement process, and (2) the generation of new states with new properties when particles become entangled. Similar problems arising with concepts motivated the formal treatment introduced (...) here. Concepts are viewed not as fixed representations, but entities existing in states of potentiality that require interaction with a context---a stimulus or another concept---to `collapse' to observable form as an exemplar, prototype, or other (possibly imaginary) instance. The stimulus situation plays the role of the measurement in physics, acting as context that induces a change of the cognitive state from superposition state to collapsed state. The collapsed state is more likely to consist of a conjunction of concepts for associative than analytic thought because more stimulus or concept properties take part in the collapse. We provide two contextual measures of conceptual distance---one using collapse probabilities and the other weighted properties---and show how they can be applied to conjunctions using the pet fish problem. (shrink)

What is absolutely unrestricted quantification? We distinguish two theoretical roles and identify two conceptions of absolute generality: maximally strong generality and maximally inclusive generality. We also distinguish two corresponding kinds of absolute domain. A maximally strong domain contains every potential counterexample to a generalisation. A maximally inclusive domain is such that no domain extends it. We argue that both conceptions of absolute generality are legitimate and investigate the relations between them. Although these conceptions coincide in standard settings, we show how (...) they diverge under more complex assumptions about the structure of meaningful predication, such as cumulative type theory. We conclude by arguing that maximally strong generality is the more theoretically valuable conception. (shrink)

There is no uniquely standard concept of an effectively decidable set of real numbers or real n-tuples. Here we consider three notions: decidability up to measure zero [M.W. Parker, Undecidability in Rn: Riddled basins, the KAM tori, and the stability of the solar system, Phil. Sci. 70(2) (2003) 359–382], which we abbreviate d.m.z.; recursive approximability [or r.a.; K.-I. Ko, Complexity Theory of Real Functions, Birkhäuser, Boston, 1991]; and decidability ignoring boundaries [d.i.b.; W.C. Myrvold, The decision problem for entanglement, in: (...) R.S. Cohen et al. (Eds.), Potentiality, Entanglement, and Passion-at-a-Distance: Quantum Mechanical Studies fo Abner Shimony, Vol. 2, Kluwer Academic Publishers, Great Britain, 1997, pp. 177–190]. Unlike some others in the literature, these notions apply not only to certain nice sets, but to general sets in Rn and other appropriate spaces. We consider some motivations for these concepts and the logical relations between them. It has been argued that d.m.z. is especially appropriate for physical applications, and on Rn with the standard measure, it is strictly stronger than r.a. [M.W. Parker, Undecidability in Rn: Riddled basins, the KAM tori, and the stability of the solar system, Phil. Sci. 70(2) (2003) 359–382]. Here we show that this is the only implication that holds among our three decidabilities in that setting. Under arbitrary measures, even this implication fails. Yet for intervals of non-zero length, and more generally, convex sets of non-zero measure, the three concepts are equivalent. (shrink)

The paper proposes a flexible way to build concepts within fuzzy logic and set theory. The framework is general enough to capture some important particular cases, with their own independent interpretations, like “antitone” or “isotone” concepts constructed from fuzzy binary relations, but also to allow the two universes to be equipped each with its own truth structure. Perhaps the most important feature of our approach is that we do not commit ourselves to any kind of logical connector, covering thus (...) the case of a possibly non-commutative conjunction too. (shrink)

The transitivity of the relation of part to whole is often questioned. But it is among the most basic principles of mereology. In this paper we present a general solution to the problem of transitivity of parthood which may be satisfactory for both its advocates and its opponents. We will show that even without the transitivity of parthood one can define—basic in mereology—the notion of being a mereological sum of some objects. We formulate several proposals of general approaches (...) to the concept of being a part of a whole, none of which contains any existential assumptions. By adding the transitivity of parthood we obtain an axiomatization of “existentially neutral” mereology. (shrink)

The term complementarity plays a central role in quantum physics, not least in various approaches to defining entanglement and the conditions for its occurrence. It has, however, been used in a variety of ways by different authors, denoting different concepts and relationships. Here we describe and clarify some of them and analyze the role they play with respect to the phenomenon of entanglement. Based on these considerations we discuss the recently proposed system-theoretical generalization of the concepts entanglement and complementarity (Atmanspacher (...) et al. in Found Phys 32(3):379–406, 2002; von Lucadou et al. in J Conscious Stud 14(4):50–74, 2007; Filk and Römer in Axiomathes 21(2):211–220, 2011; Walach and Von Stillfried in Axiomathes 21(2): 185–209, 2011). We hope that a clarification regarding the specific meaning of these terms can be useful to the growing engagement with this interesting hypothesis and its critical investigation. (shrink)

The term complementarity plays a central role in quantum physics, not least in various approaches to defining entanglement and the conditions for its occurrence. It has, however, been used in a variety of ways by different authors, denoting different concepts and relationships. Here we describe and clarify some of them and analyze the role they play with respect to the phenomenon of entanglement. Based on these considerations we discuss the recently proposed system-theoretical generalization of the concepts entanglement and complementarity (Atmanspacher (...) et al. in Found Phys 32(3):379–406, 2002; von Lucadou et al. in J Conscious Stud 14(4):50–74, 2007; Filk and Römer in Axiomathes 21(2):211–220, 2011; Walach and Von Stillfried in Axiomathes 21(2): 185–209, 2011). We hope that a clarification regarding the specific meaning of these terms can be useful to the growing engagement with this interesting hypothesis and its critical investigation. (shrink)

Generalized trust is widely said to be essential for social and economic cooperation, but—despite the large empirical literature—there is disagreement and confusion over how to understand generalized trust. This paper develops the conceptual options that can be drawn from the social science literature—with attention to the moral dimension in each, and with some attention to the different ways that generalized trust can serve as a foundation for the social order.

The idea of a text is reviewed and reconstructed to facilitate the application of concepts of interpretation to the objects analyzed in the natural sciences, as well as to objects analyzed in religion and literature. Four criteria—‐readability, formality, material transcendence, and retrievability—‐are proposed as the basis for a generalized conception of text. Objects in both religion and science, not previously thought to be texts, are shown to be included in the new definition and therefore to be potential subjects of developing (...) methods of interpretation. (shrink)

In the Tractatus, Wittgenstein describes the general validity of logical truths as being “essential,” as opposed to merely “accidental” general truths. He does not say much more, and little has been said about it by commentators. How to make sense of the essential general validity by which Wittgenstein characterizes logic? This chapter aims to clarify this crucial concept.