Interlevel Relations in Biology, Misc

One important aspect of biological explanation is detailed causal modeling of particular phenomena in limited experimental background conditions. Recognising this allows a new avenue for intertheoretic reduction to be seen. Reductions in biology are possible, when one fully recognises that a sufficient condition for a reduction in biology is a molecular model of 1) only the demonstrated causal parameters of a biological model and 2) only within a replicable experimental background. These intertheoretic identifications –which are ubiquitous in biology and form (...) the basis of ruthless reductions (Bickle 2003)- are criticised as merely “local” (Sullivan 2009) or “fragmentary” (Schaffner 2006). However, in an instructive case, a biological model is preserved in molecular terms, and a complex biological phenomenon has been successfully reduced. In doing this the molecular model remains valid in a broader range of background conditions and meaningfully unites disparate biological phenomena. (shrink)

The levels of selection debate is generally taken to be a debate about how natural selection can occur at the various levels of biological organization. In this paper, we argue that questions about levels of selection should be analyzed separately from questions about levels of organization. In the deflationary proposal we defend, all that is necessary for multilevel selection is that there are cases in which particles are nested in collectives, and that both the collectives and the particles that compose (...) them each separately undergo natural selection. We argue that adopting this deflationary account helps to disentangle the levels of selection and the levels of organization, and thereby contributes to advancing the levels of selection debate. (shrink)

I attempt to characterize the relationship of classical experimental embryology (CEE) and molecular developmental biology and compare it to the much-discussed case of classical genetics. These sciences are treated here as discovery practices rather than as definitive forms of knowledge. I first show that CEE had some causal knowledge and hence was able to answer specific why?-questions. A paradigm was provided by the case of eye induction, perhaps CEE’s greatest success. The case of the famous Spemann-Mangold organizer is more difficult. (...) I argue that before the advent of molecular biology, knowledge of its causal role in development was very limited. As a result, there was no functional definition of the concept of organizer. I argue that, like the classical gene concept, it is best viewed as an operational concept. This means that an account of reduction such as Kim’s functional reduction, which is still a mainstay in scientific metaphysics, cannot work in these cases. Nonetheless, again like in the classical gene case, the operational concepts of CEE played an important heuristic role in the discovery of molecules involved in morphogenesis and cell differentiation. This was made possible by what I call inter-level investigative practices. These are practices that combine experimental manipulations targeting two (or more) different levels. I conclude that the two sciences are more closely related via their experimental practices than by any inter-level explanatory relations. (shrink)

Following its initial development in the 1920’s and 1930’s, by mid-century the concept of “levels of organization” began to disperse throughout the life science textbook literature. Among other early textbooks that first applied the levels concept, Eugene P. Odum’s usage of the notion in his textbook series Fundamentals of Ecology (and his later series Ecology) stands out due to the marked emphasis placed on the concept as a foundational, erotetically-oriented organizing principle. In this paper, I examine Odum’s efforts toward advocating (...) the levels concept in ecology in light of the concept’s wider uptake in biology around that time. (shrink)

We provide three innovations to recent debates about whether topological or “network” explanations are a species of mechanistic explanation. First, we more precisely characterize the requirement that all topological explanations are mechanistic explanations and show scientific practice to belie such a requirement. Second, we provide an account that unifies mechanistic and non-mechanistic topological explanations, thereby enriching both the mechanist and autonomist programs by highlighting when and where topological explanations are mechanistic. Third, we defend this view against some powerful mechanist objections. (...) We conclude from this that topological explanations are autonomous from their mechanistic counterparts. (shrink)

Changes in synaptic strength are described as a unifying hypothesis for memory formation and storage, leading philosophers to consider the ‘synaptic efficacy hypothesis’ as a paradigmatic explanation in neuroscience. Craver’s mosaic view has been influential in understanding synaptic efficacy by presenting long-term potentiation as a multi-level mechanism nested within a multi-level structure. This paper argues that the mosaic view fails to fully capture the explanatory power of the synaptic efficacy hypothesis due to assumptions about multi-level mechanisms. I present an alternative (...) approach that emphasizes the explanatory function of unification, accounting for the widespread consensus in neuroscience regarding synaptic efficacy by highlighting the stability of synaptic causal variables across different multi-level mechanisms. (shrink)

(Back Cover:) « La pensée métaphysique renaîtra demain. Ce sont des savants qui ont le goût et le sens de la pensée conduite jusqu’au terme de ses exigences internes, et des philosophes initiés aux sciences expérimentales qui, en commun, la feront. » L’œuvre de Claude Tresmontant (1925-1997) illustre parfaitement cette recherche de la métaphysique d’un monde en devenir, qui sait écouter et se modeler sur la transformation – la métamorphose – promise à une Création finalisée. Le trait commun aux exposés (...) ici présentés sous forme définitive a été cette recherche autour d’une pensée qui renouvelle de l’intérieur la métaphysique en réalisant le vœu de Bergson qu’elle devienne « auscultatrice », que l’énigme que pose l’homme face à son origine et sa destinée ne soit pas recouverte par une pensée qui se perdrait dans la description des choses ou dans l’esprit de système, mais qui non plus n’irait se recroqueviller sur elle-même, en narrant sa propre expérience subjective sous le mode de la déréliction. Claude Tresmontant a su penser l’être en genèse, et il a cherché à renouveler la question de l’existence de Dieu, en en transformant la problématique en dialogue avec les sciences contemporaines. À ce goût de l’être dont les sciences ont renouvelé l’approche, il a également voulu infuser un « supplément d’âme », en repensant la réalité de la création et l’horizon de la cause finale, toujours à partir de la nature ultimement théologique de la réponse à la question « qu’est-ce que l’homme ? » Contributeurs : Yves Tourenne, Philippe Gagnon, Fabien Revol, Brunor, Frédéric Crouslé, Bertrand Souchard, Emmanuel Gabellieri. Table of Contents: Note Liminaire (Ph. Gagnon) - 7 En quoi la pensée de Claude Tresmontant nous stimule-t-elle encore ? Hommage et critique (Y. Tourenne) - 13 L’imbrication de la preuve de Dieu et de la cosmologie chez Tresmontant représente-t-elle une preuve ? (Ph. Gagnon) - 27 L’usage apologétique de la philosophie de Tresmontant dans les Indices pensables de Brunor (F. Revol) - 49 Réponse à Fabien Revol (Brunor) - 77 Qu’est-ce qui cloche dans la théologie de Claude Tresmontant ? (Fr. Crouslé) - 85 Les métaphysiques principales de Claude Tresmontant : la foi biblique est-elle à part de la raison philosophique grecque ? (B. Souchard) - 109 Maurice Blondel et Claude Tresmontant (E. Gabellieri) - 123 La vision informationnelle de Tresmontant, surtout en référence au problème de l’âme (Ph. Gagnon) - 133. (shrink)

The history of developmental biology is interwoven with debates as to whether mechanistic explanations of development are possible or whether alternative explanatory principles or even vital forces need to be assumed. In particular, the demonstrated ability of embryonic cells to tune their developmental fate precisely to their relative position and the overall size of the embryo was once thought to be inexplicable in mechanistic terms. Taking a causal perspective, this Element examines to what extent and how developmental biology, having turned (...) molecular about four decades ago, has been able to meet the vitalist challenge. It focuses not only on the nature of explanations but also on the usefulness of causal knowledge – including the knowledge of classical experimental embryology – for further scientific discovery. It also shows how this causal perspective allows us to understand the nature and significance of some key concepts, including organizer, signal and morphogen. This title is also available as Open Access on Cambridge Core. (shrink)

Debates concerning the units and levels of selection have persisted for over fifty years. One major question in this literature is whether units and levels of selection are genuine, in the sense that they are objective features of the world, or merely reflect the interests and goals of an observer. Scientists and philosophers have proposed a range of answers to this question. This Element introduces this literature and proposes a novel contribution. It defends a realist stance and offers a way (...) of delineating genuine levels of selection by invoking the notion of a functional unit. (shrink)

An adequate understanding of the ubiquitous practice of mechanistic explanation requires an account of what Craver termed “constitutive relevance.” Entities or activities are constitutively relevant to a phenomenon when they are parts of the mechanism responsible for that phenomenon. Craver’s mutual manipulability account extended Woodward’s account of manipulationist counterfactuals to analyze how interlevel experiments establish constitutive relevance. Critics of MM argue that applying Woodward’s account to this philosophical problem conflates causation and constitution, thus rendering the account incoherent. These criticisms, we (...) argue, arise from failing to distinguish the semantic, epistemic, and metaphysical aspects of the problem of constitutive relevance. In distinguishing these aspects of the problem and responding to these critics accordingly, we amend MM into a refined epistemic criterion, the “matched interlevel experiments” account. Further, we explain how this epistemological thesis is grounded in the plausible metaphysical thesis that constitutive relevance is causal betweenness. (shrink)

Islam gives legal precedence to purity of lineage and known parenthood of all children. In Islam treatment to infertility using IVF is permitted within validity of marriage contract with no genes mixing. The paper shows that the Qur’ān, the word of Allah, and science, the deeds of Allah are not in major conflicts in defining the start of human life. The Holy Qur’ān provides an elegant description of origin, developmental stages of intra-uterine life. The Hadith explains two positions one that (...) believes human embryo get ensouled at conception and the other after 40 days of conception. The paper aims to find that Islam confers moral respect to human embryo, but it also clarifies the absence of full human rights to a developing foetus. In Islam, human embryonic use is probably permissible for therapeutic and reproductive purpose keeping intact the principles of Shari’ah. (shrink)

Recent arguments concerning the nature of causation in evolutionary theory, now often known as the debate between the 'causalist' and 'statisticalist' positions, have involved answers to a variety of independent questions – definitions of key evolutionary concepts like natural selection, fitness, and genetic drift; causation in multi-level systems; or the nature of evolutionary explanations, among others. This Element offers a way to disentangle one set of these questions surrounding the causal structure of natural selection. Doing so allows us to clearly (...) reconstruct the approach that some of these major competing interpretations of evolutionary theory have to this causal structure, highlighting particular features of philosophical interest within each. Further, those features concern problems not exclusive to the philosophy of biology. Connections between them and, in two case studies, contemporary metaphysics and philosophy of physics demonstrate the potential value of broader collaboration in the understanding of evolution. (shrink)

The extent to which normal (nonmalignant) cells of the body can evolve through mutation and selection during the lifetime of the organism has been a major unresolved issue in evolutionary and developmental studies. On the one hand, stable multicellular individuality seems to depend on genetic homogeneity and suppression of evolutionary conflicts at the cellular level. On the other hand, the example of clonal selection of lymphocytes indicates that certain forms of somatic mutation and selection are concordant with the organism-level fitness. (...) Recent DNA sequencing and tissue physiology studies suggest that in addition to adaptive immune cells also neurons, epithelial cells, epidermal cells, hematopoietic stem cells and functional cells in solid bodily organs are subject to evolutionary forces during the lifetime of an organism. Here we refer to these recent studies and suggest that the expanding list of somatically evolving cells modifies idealized views of biological individuals as radically different from collectives. (shrink)

Precision medicine and molecular systems medicine (MSM) are highly utilized and successful approaches to improve understanding, diagnosis, and treatment of many diseases from bench-to-bedside. Especially in the COVID-19 pandemic, molecular techniques and biotechnological innovation have proven to be of utmost importance for rapid developments in disease diagnostics and treatment, including DNA and RNA sequencing technology, treatment with drugs and natural products and vaccine development. The COVID-19 crisis, however, has also demonstrated the need for systemic thinking and transdisciplinarity and the limits (...) of MSM: the neglect of the bio-psycho-social systemic nature of humans and their context as the object of individual therapeutic and population-oriented interventions. COVID-19 illustrates how a medical problem requires a transdisciplinary approach in epidemiology, pathology, internal medicine, public health, environmental medicine, and socio-economic modeling. Regarding the need for conceptual integration of these different kinds of knowledge we suggest the application of general system theory (GST). This approach endorses an organism-centered view on health and disease, which according to Ludwig von Bertalanffy who was the founder of GST, we call Organismal Systems Medicine (OSM). We argue that systems science offers wider applications in the field of pathology and can contribute to an integrative systems medicine by (i) integration of evidence across functional and structural differentially scaled subsystems, (ii) conceptualization of complex multilevel systems, and (iii) suggesting mechanisms and non-linear relationships underlying the observed phenomena. We underline these points with a proposal on multi-level systems pathology including neurophysiology, endocrinology, immune system, genetics, and general metabolism. An integration of these areas is necessary to understand excess mortality rates and polypharmacological treatments. In the pandemic era this multi-level systems pathology is most important to assess potential vaccines, their effectiveness, short-, and long-time adverse effects. We further argue that these conceptual frameworks are not only valid in the COVID-19 era but also important to be integrated in a medicinal curriculum. (shrink)

Endocrinologists apply the idea of feedback loops to explain how hormones regulate certain bodily functions such as glucose metabolism. In particular, feedback loops focus on the maintenance of the plasma concentrations of glucose within a narrow range. Here, we put forward a different, organicist perspective on the endocrine regulation of glycaemia, by relying on the pivotal concept of closure of constraints. From this perspective, biological systems are understood as organized ones, which means that they are constituted of a set of (...) mutually dependent functional structures acting as constraints, whose maintenance depends on their reciprocal interactions. Closure refers specifically to the mutual dependence among functional constraints in an organism. We show that, when compared to feedback loops, organizational closure can generate much richer descriptions of the processes and constraints at play in the metabolism and regulation of glycaemia, by making explicit the different hierarchical orders involved. We expect that the proposed theoretical framework will open the way to the construction of original mathematical models, which would provide a better understanding of endocrine regulation from an organicist perspective. (shrink)

In this work I propose a theory of evolution as a process of unfolding. This theory is based on four logically concatenated principles. The principle of evolutionary order establishes that the more complex cannot be generated from the simpler. The principle of origin establishes that there must be a maximum complexity that originates the others by logical deduction. Finally, the principle of unfolding and the principle of actualization guarantee the development of the evolutionary process from the simplest to the most (...) complex. These logical principles determine the existence of a virtual ideological matrix that contains the sequence of the preformed and folded morphogenetic fields. In this manner, the evolutionary process consists of the sequential unfolding and actualization of these fields, which is motorized by a process of teleologization carried out by the opening consciousness of the forms included in the fields of the ideological matrix. This theory leads to a radical change of perspective regarding the materialist worldview, and places life at the center of the evolutionary process as an activity carried out by a consciousness that seeks to fulfill a purpose by actualizing its own potentialities. (shrink)

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

A holobiont is a composite organism consisting of a host together with its microbiome, such as a coral with its zooxanthellae. To explain the often intimate integration between hosts and their microbiomes, some investigators contend that selection operates on holobionts as a unit and view the microbiome’s genes as extending the host’s nuclear genome to jointly comprise a hologenome. Because vertical transmission of microbiomes is uncommon, other investigators contend that holobiont selection cannot be effective because a holobiont’s microbiome is an (...) acquired condition rather than an inherited trait. This disagreement invites a simple mathematical model to see how holobiont selection might operate and to assess its plausibility as an evolutionary force. This paper presents two variants of such a model. In one variant, juvenile hosts obtain microbiomes from their parents (vertical transmission). In the other variant, microbiomes of juvenile hosts are assembled from source pools containing the combined microbiomes of all parents (horizontal transmission). According to both variants, holobiont selection indeed causes evolutionary change in holobiont traits. Therefore, holobiont selection is plausibly an effective evolutionary force with either mode of microbiome transmission. The modeling employs two distinct concepts of inheritance, depending on the mode of microbiome transmission: collective inheritance whereby juveniles inherit a sample of the collected genomes from all parents, as contrasted with lineal inheritance whereby juveniles inherit the genomes from only their own parents. A distinction between collective and lineal inheritance also features in theories of multilevel selection. (shrink)

Philosophy of immunology is a subfield of philosophy of biology dealing with ontological and epistemological issues related to the studies of the immune system. While speculative investigations and abstract analyses have always been part of immune theorizing, until recently philosophers have largely ignored immunology. Yet the implications for understanding the philosophical basis of organismal functions framed by immunity offer new perspectives on fundamental questions of biology and medicine. Developed in the context of history of medicine, theoretical biology, and medical anthropology, (...) philosophy of immunology differs from these related branches of study in its focus on traditional philosophical questions concerning identity, individuality, ecology, cognition, scientific methodology and theory construction. This broad agenda derives from immunology’s multifaceted research program that has developed from its initial clinical challenges of host defense, transplantation, autoimmunity, tumor immunology, and allergy. In addition to these well-established research areas, immunity is now understood to play a central role in other physiological functions, development, ecology, and evolutionary mechanics. Holding together these diverse domains of inquiry lie philosophical commitments oriented by organismal identity. In this regard, pertinent issues are raised concerning cognition (organization of immune perception and information processing), the character of individuality (framed by the ecological context of immune-mediated assimilation and rejection), and the dynamics of complex systems (understood as holistic systems biology). Indeed, immunology, in the context of cognitive science, evolutionary biology, environmental sciences, and development provides multi-focal perspectives for philosophy of science. (shrink)

Critics of multiple realizability have recently argued that we should concentrate solely on actual here-and-now realizations that are found in nature. The possibility of alternative, but unactualized, realizations is regarded as uninteresting because it is taken to be a question of pure logic or an unverifiable scenario of science fiction. However, in the biological context only a contingent set of realizations is actualized. Drawing on recent work on the theory of neutral biological spaces, the paper shows that we can have (...) ways of assessing the modal dimension of multiple realizability that do not have to rely on mere conceivability. (shrink)

We introduce a new type of pluralism about biological function that, in contrast to existing, demonstrates a practical integration among the term’s different meanings. In particular, we show how to generalize Sandra Mitchell’s notion of integrative pluralism to circumstances where multiple epistemic tools of the same type are jointly necessary to solve scientific problems. We argue that the multiple definitions of biological function operate jointly in this way based on how biologists explain the evolution of protein function. To clarify how (...) our account relates to existing views, we introduce a general typology for monist and pluralist accounts along with standardized criteria for judging which is best supported by evidence. (shrink)

In the last decade, Systems Biology has emerged as a conceptual and explanatory alternative to reductionist-based approaches in molecular biology. However, the foundations of this new discipline need to be fleshed out more carefully. In this paper, we claim that a relational ontology is a necessary tool to ground both the conceptual and explanatory aspects of Systems Biology. A relational ontology holds that relations are prior—both conceptually and explanatory—to entities, and that in the biological realm entities are defined primarily by (...) the context they are embedded within—and hence by the web of relations they are part of. (shrink)

his monograph examines the metaphysical commitments of the new mechanistic philosophy, a way of thinking that has returned to center stage. It challenges a variant of reductionism with regard to higher-level phenomena, which has crystallized as a default position among these so-called New Mechanists. Furthermore, it opposes those philosophers who reject the possibility of interlevel causation. Contemporary philosophers believe that the explanation of scientific phenomena requires the discovery of relevant mechanisms. As a result, new mechanists are, in the main, concerned (...) solely with epistemological questions. But, the author argues, their most central claims rely on metaphysical assumptions. Thus, they must also take into account metaphysics, a system of thought concerned with explaining the fundamental nature of being and the world around it. This branch of philosophy does indeed matter to the empirical sciences. The chapters investigate the nature of mechanisms, their components, and the ways in which they can bring about different phenomena. In addition, the author develops a novel account of causation in terms of activities. The analysis provides the basis for many further research projects on mechanisms and their relations to, for example, the mind-body problem, realization, multiple realization, natural kinds, causation, laws of nature, counterfactuals, and scientific levels. (shrink)

Starting with the observation that there exist contradictory claims in the literature about the relationship between vitalism and emergentism—be it one of inclusion or, on the contrary, exclusion–, this paper aims at disentangling the vitalism–emergentism knot. To this purpose, after having described a particular form of emergentism, namely Lloyd Morgan’s emergent evolutionism, I develop a conceptual analysis on the basis of a distinction between varieties of monism and pluralism. This analysis allows me to identify and characterize several forms of vitalism (...) and emergentism, and a subsequent comparison between these forms constitutes the occasion for a clarification of the relationship between both doctrines. (shrink)

I argue (1) that what (ontic) New Mechanistic philosophers of science call mechanisms would be material Gestalten, and (2) that Merleau-Ponty’s engagement with Gestalt theory can help us frame a standing challenge against ontic conceptions of mechanisms. In short, until the (ontic) New Mechanist can provide us with a plausible account of the organization of mechanisms as an objective feature of mind-independent ontic structures in the world which we might discover – and no ontic Mechanist has done so – it (...) is more conservative to claim that mechanistic organization is instead a mind-dependent aspect of our epistemic strategies of mechanistic explanation. (shrink)

Existing accounts of mechanistic causation are not suited for understanding causation in biological and neural mechanisms because they do not have the resources to capture the unique causal structure of control heterarchies. In this paper, we provide a new account on which the causal powers of mechanisms are grounded by time-dependent, variable constraints. Constraints can also serve as a key bridge concept between the mechanistic approach to explanation and underappreciated work in theoretical biology that sheds light on how biological systems (...) channel energy to actively respond to the environment in adaptive ways, perform work, and fulfill the requirements to maintain themselves far from equilibrium. We show how the framework applies to several concrete examples of control in simple organisms as well as the nervous system of complex organisms. (shrink)

This paper responds to recent criticisms of the idea that true causal claims, satisfying a minimal “interventionist” criterion for causation, can differ in the extent to which they satisfy other conditions—called stability and proportionality—that are relevant to their use in explanatory theorizing. It reformulates the notion of proportionality so as to avoid problems with previous formulations. It also introduces the notion of conditional independence or irrelevance, which I claim is central to understanding the respects and the extent to which upper (...) level explanations can be “autonomous”. (shrink)

The first part of this paper finds Craver’s (2007) mutual manipulability theory (MM) of constitution inadequate, as it definitionally ties constitution to the feasibility of idealized experiments, which, however, are unrealizable in principle. As an alternative, the second part develops an abductive theory of constitution (NDC), which exploits the fact that phenomena and their constituents are unbreakably coupled via common causes. The best explanation for this common-cause coupling is the existence of an additional dependence relation, viz. constitution. Apart from adequately (...) capturing the essential characteristics of constitution missed by MM, NDC has important ramifications for constitutional discovery—most notably, that there is no experimentum crucis for constitution, not even under ideal discovery circumstances. (shrink)

Despite the ubiquity of “levels of organization” in the scientific literature, a nascent “levels skepticism” now claims that the concept of levels is an inherently flawed, misleading, or otherwise inadequate notion for understanding how life scientists produce knowledge about the natural world. However, levels skeptics rely on the maligned “layer-cake” account of levels stemming from Oppenheim and Putnam’s defense of the unity of science for their critical commentary. Recourse to layer-cake levels is understandable, as it is arguably the default conception (...) of levels in philosophy. However, relying on this conception of levels undermines the initial plausibility of general dismissals of the concept, because the problems skeptics identify within the “basic idea” of the concept “levels” are merely ones already widely acknowledged in this conception. I illustrate this “guilt by association” by looking at the embedded role of “levels” in articulating intertheoretical reductionism during the latter part of the 20th century. I conclude by suggesting a methodological framework focusing on local usage patterns as a promising means for future analysis of the levels concept. (shrink)

Courtesy of its free energy formulation, the hierarchical predictive processing theory of the brain (PTB) is often claimed to be a grand unifying theory. To test this claim, we examine a central case: activity of mesocorticolimbic dopaminergic (DA) systems. After reviewing the three most prominent hypotheses of DA activity—the anhedonia, incentive salience, and reward prediction error hypotheses—we conclude that the evidence currently vindicates explanatory pluralism. This vindication implies that the grand unifying claims of advocates of PTB are unwarranted. More generally, (...) we suggest that the form of scientific progress in the cognitive sciences is unlikely to be a single overarching grand unifying theory. (shrink)

The premise of biological modularity is an ontological claim that appears to come out of practice. We understand that the biological world is modular because we can manipulate different parts of organisms in ways that would only work if there were discrete parts that were interchangeable. This is the foundation of the BioBrick assembly method widely used in synthetic biology. It is one of a number of methods that allows practitioners to construct and reconstruct biological pathways and devices using DNA (...) libraries of standardized parts with known functions. In this paper, we investigate how the practice of synthetic biology reconfigures biological understanding of the key concepts of modularity and evolvability. We illustrate how this practice approach takes engineering knowledge and uses it to try to understand biological organization by showing how the construction of functional parts and processes can be used in synthetic experimental evolution. We introduce a new approach within synthetic biology that uses the premise of a parts-based ontology together with that of organismal self-organization to optimize orthogonal metabolic pathways in E. coli. We then use this and other examples to help characterize semisynthetic categories of modularity, parthood, and evolvability within the discipline. (shrink)

According to the new mechanistic approach, an acting entity is at a lower mechanistic level than another acting entity if and only if the former is a component in the mechanism for the latter. Craver and Bechtel :547–563, 2007. doi:10.1007/s10539-006-9028-8) argue that a consequence of this view is that there cannot be causal interactions between acting entities at different mechanistic levels. Their main reason seems to be what I will call the Metaphysical Argument: things at different levels of a mechanism (...) are related as part and whole; wholes and their parts cannot be related as cause and effect; hence, interlevel causation in mechanisms is impossible. I will analyze this argument in more detail and show under which conditions it is valid. This analysis will reveal that interlevel causation in mechanisms is indeed possible, if we take seriously the idea that the relata of the mechanistic level relation are acting entities and accept a slightly modified notion of a mechanistic level that is highly plausible in the light of the first clarification. (shrink)

Some recent accounts of constitutive relevance have identified mechanism components with entities that are causal intermediaries between the input and output of a mechanism. I argue that on such accounts there is no distinctive inter-level form of mechanistic explanation and that this highlights an absence in the literature of a compelling argument that there are such explanations. Nevertheless, the entities that these accounts call ‘components’ do play an explanatory role. Studying causal intermediaries linking variables Xand Y provides knowledge of the (...) counterfactual conditions under which X will continue to bring about Y. This explanatory role does not depend on whether intermediate variables count as components. The question of whether there are distinctively mechanistic explanations remains open. (shrink)

This chapter discusses several kinds of reduction that are often found in the biomedical sciences, in contrast to reduction in fields such as physics. This includes reduction as a methodological assumption for how to investigate phenomena like complex diseases, and reduction as a conceptual tool for relating distinct models of the same phenomenon. The case of Parkinson’s disease illustrates a wide variety of ways in which reductionism is an important tool in medicine.

The idea of levels of organization plays a central role in the philosophy of the life sciences. In this article, I first examine the explanatory goals that have motivated accounts of levels of organization. I then show that the most state-of-the-art and scientifically plausible account of levels of organization, the account of levels of mechanism proposed by Bechtel and Craver, is fundamentally problematic. Finally, I argue that the explanatory goals can be reached by adopting a deflationary approach, where levels of (...) organization give way to more well-defined and fundamental notions, such as scale and composition. (shrink)

Life has semiotic nature; and as life forms differ in their complexity, functionality, and adaptability, we assume that forms of semiosis also vary accordingly. Here we propose a criterion to distinguish between the primitive kind of semiosis, which we call “protosemiosis” from the advanced kind of semiosis, or “eusemiosis”. In protosemiosis, agents associate signs directly with actions without considering objects, whereas in eusemiosis, agents associate signs with objects and only then possibly with actions. Protosemiosis started from the origin of life, (...) and eusemiosis started when evolving agents acquired the ability to track and classify objects. Eusemiosis is qualitatively different from protosemiosis because it can not be reduced to a small number of specific signaling pathways. Proto-signs can be classified into proto-icons that signal via single specific interaction, proto-indexes that combine several functions, and proto-symbols that are processed by a universal subagent equipped with a set of heritable adapters. Prefix “proto” is used here to characterize signs at the protosemiotic level. Although objects are not recognized by protosemiotic agents, they can be reliably reconstructed by human observers. In summary, protosemiosis is a primitive kind of semiosis that supports “know-how” without “know-what”. Without studying protosemiosis, the biosemiotics theory would be incomplete. (shrink)

Analogies to machines are commonplace in the life sciences, especially in cellular and molecular biology — they shape conceptions of phenomena and expectations about how they are to be explained. This paper offers a framework for thinking about such analogies. The guiding idea is that machine-like systems are especially amenable to decompositional explanation, i.e., to analyses that tease apart underlying components and attend to their structural features and interrelations. I argue that for decomposition to succeed a system must exhibit causal (...) orderliness, which I explicate in terms of differentiation among parts and the significance of local relations. I also discuss what makes a model depict its target as machine-like, suggesting that a key issue is the degree of detail with respect to the target’s parts and their interrelations. (shrink)

Emergent antireductionism in biological sciences states that even though all living cells and organisms are composed of molecules, molecular wholes are characterized by emergent properties that can only be understood from the perspective of cellular and organismal levels of composition. Thus, an emergence claim (molecular wholes are characterized by emergent properties) is thought to support a form of antireductionism (properties of higher-level molecular wholes can only be understood by taking into account concepts, theories and explanations dealing with higher-level entities). I (...) argue that this argument is flawed: even if molecular wholes are characterized by emergent properties and even if many successful explanations in biology are not molecular, there is no entailment between the two claims. (shrink)

In this paper I argue that it is finally time to move beyond the Nagelian framework and to break new ground in thinking about epistemic reduction in biology. I will do so, not by simply repeating all the old objections that have been raised against Ernest Nagel’s classical model of theory reduction. Rather, I grant that a proponent of Nagel’s approach can handle several of these problems but that, nevertheless, Nagel’s general way of thinking about epistemic reduction in terms of (...) theories and their logical relations is entirely inadequate with respect to what is going on in actual biological research practice. (shrink)

This paper aims to identify the key characteristics of model organisms that make them a specific type of model within the contemporary life sciences: in particular, we argue that the term “model organism” does not apply to all organisms used for the purposes of experimental research. We explore the differences between experimental and model organisms in terms of their material and epistemic features, and argue that it is essential to distinguish between their representational scope and representational target. We also examine (...) the characteristics of the communities who use these two types of models, including their research goals, disciplinary affiliations, and preferred practices to show how these have contributed to the conceptualization of a model organism. We conclude that model organisms are a specific subgroup of organisms that have been standardized to fit an integrative and comparative mode of research, and that it must be clearly distinguished from the broader class of experimental organisms. In addition, we argue that model organisms are the key components of a unique and distinctively biological way of doing research using models.Keywords: Experimental organism; Genetics; Model organism; Modeling; Philosophy of biology; Representation. (shrink)

This book presents programmatic texts on biosemiotics, written collectively by world leading scholars in the field (Deacon, Emmeche, Favareau, Hoffmeyer, Kull, Markoš, Pattee, Stjernfelt). In addition, the book includes chapters which focus closely on semiotic case studies (Bruni, Kotov, Maran, Neuman, Turovski). According to the central thesis of biosemiotics, sign processes characterise all living systems and the very nature of life, and their diverse phenomena can be best explained via the dynamics and typology of sign relations. The authors are therefore (...) presenting a deeper view on biological evolution, intentionality of organisms, the role of communication in the living world and the nature of sign systems - all topics which are described in this volume. This has important consequences on the methodology and epistemology of biology and study of life phenomena in general, which the authors aim to help the reader better understand. (shrink)

The inapplicability of variations on theory reduction in the context of genetics and their irrelevance to ongoing research has led to an anti-reductionist consensus in philosophy of biology. One response to this situation is to focus on forms of reductive explanation that better correspond to actual scientific reasoning (e.g. part–whole relations). Working from this perspective, we explore three different aspects (intrinsicality, fundamentality, and temporality) that arise from distinct facets of reductive explanation: composition and causation. Concentrating on these aspects generates new (...) forms of reductive explanation and conditions for their success or failure in biology and other sciences. This analysis is illustrated using the case of protein folding in molecular biology, which demonstrates its applicability and relevance, as well as illuminating the complexity of reductive reasoning in a specific biological context. (shrink)

Symmetries play a major role in physics, in particular since the work by E. Noether and H. Weyl in the first half of last century. Herein, we briefly review their role by recalling how symmetry changes allow to conceptually move from classical to relativistic and quantum physics. We then introduce our ongoing theoretical analysis in biology and show that symmetries play a radically different role in this discipline, when compared to those in current physics. By this comparison, we stress that (...) symmetries must be understood in relation to conservation and stability properties, as represented in the theories. We posit that the dynamics of biological organisms, in their various levels of organization, are not just processes, but permanent (extended, in our terminology) critical transitions and, thus, symmetry changes. Within the limits of a relative structural stability (or interval of viability), variability is at the core of these transitions. (shrink)

We summarise the contributions to the discussion and the links between them. The complex relationship between the physical and biological sciences demonstrates three “axes of tension”: the role of simulation, the interplay between levels of explanation, and the generality of “laws”. We identify examples of true synergy between approaches that genuinely explore new research territory, and underscore the contemporary value of the type of discussions contained in this volume.

The immune system, to protect the body, must discriminate between the pathogenic and non-pathogenic microbes and respond to them in different ways. How the mucosal immune system manages to make this distinction is poorly understood. We suggest here that the distinction between pathogenic and non-pathogenic microbes is made by an integrated system rather than by single types of cells or single types of receptors; a systems biology approach is needed to understand immune recognition.

In Making Sense of Life , Keller emphasizes several differences between biology and physics. Her analysis focuses on significant ways in which modelling practices in some areas of biology, especially developmental biology, differ from those of the physical sciences. She suggests that natural models and modelling by homology play a central role in the former but not the latter. In this paper, I focus instead on those practices that are importantly similar, from the point of view of epistemology and cognitive (...) science. I argue that concrete and abstract models are significant in both disciplines, that there are shared selection criteria for models in physics and biology, e.g. familiarity, and that modelling often occurs in a similar fashion. (shrink)

Reductionism encompasses a set of ontological, epistemological, and methodological claims about the relation of different scientific domains. The basic question of reduction is whether the properties, concepts, explanations, or methods from one scientific domain (typically at higher levels of organization) can be deduced from or explained by the properties, concepts, explanations, or methods from another domain of science (typically one about lower levels of organization). Reduction is germane to a variety of issues in philosophy of science, including the structure of (...) scientific theories, the relations between different scientific disciplines, the nature of explanation, the diversity of methodology, and the very idea of theoretical progress, as well as to numerous topics in metaphysics and philosophy of mind, such as emergence, mereology, and supervenience. (shrink)