This open access book assesses the prospects of (re)adopting organization as a pivotal concept in biology. It shows how organization can nourish biological thinking and practice, by reconnecting with the idea of biology as the science of organized systems. The book provides a comprehensive state-of-the-art picture of the characterizations and uses of the concept of organization in both biological science and philosophy of biology. It also deals with a variety of themes – including evolution, organogenesis, heredity, cognition and ecology – (...) with respect to which the concept of organization can guide the elaboration of original models and new experimental protocols. It will be of interest to biologists and scholars working in philosophy of science alike. (shrink)

Ecological and sensorimotor theories of perception build on the notion of action-dependent invariants as the basic structures underlying perceptual capacities. In this paper we contrast the assumptions these theories make on the nature of perceptual information modulated by action. By focusing on the question, how movement specifies perceptual information, we show that ecological and sensorimotor theories endorse substantially different views about the role of action in perception. In particular we argue that ecological invariants are characterized with reference to transformations produced (...) in the sensory array by movement: such invariants are transformation-specific but do not imply motor-specificity. In contrast, sensorimotor theories assume that perceptual invariants are intrinsically tied to specific movements. We show that this difference leads to different empirical predictions and we submit that the distinction between motor equivalence and motor-specificity needs further clarification in order to provide a more constrained account of action/perception relations. (shrink)

In this paper, we develop an organizational account that defines biological functions as causal relations subject to closure in living systems, interpreted as the most typical example of organizationally closed and differentiated self-maintaining systems. We argue that this account adequately grounds the teleological and normative dimensions of functions in the current organization of a system, insofar as it provides an explanation for the existence of the function bearer and, at the same time, identifies in a non-arbitrary way the norms that (...) functions are supposed to obey. Accordingly, we suggest that the organizational account combines the etiological and dispositional perspectives in an integrated theoretical framework. IntroductionDispositional ApproachesEtiological TheoriesBiological Self-maintenance Closure, teleology, and normativityOrganizational differentiationFunctions C1: Contributing to the maintenance of the organization C2: Producing the functional trait Implications and Objections Functional versus useful Dysfunctions, side effects, and accidental contributionsProper functions and selected effectsReproductionRelation with other ‘unitarian’ approachesConclusions. (shrink)

This paper argues that biological organisation can be legitimately conceived of as an intrinsically teleological causal regime. The core of the argument consists in establishing a connection between organisation and teleology through the concept of self-determination: biological organisation determines itself in the sense that the effects of its activity contribute to determine its own conditions of existence. We suggest that not any kind of circular regime realises self-determination, which should be specifically understood as self-constraint: in biological systems, in particular, self-constraint (...) takes the form of closure, i.e. a network of mutually dependent constitutive constraints. We then explore the occurrence of intrinsic teleology in the biological domain and beyond. On the one hand, the organisational account might possibly concede that supra-organismal biological systems could realise closure, and hence be teleological. On the other hand, the realisation of closure beyond the biological realm appears to be highly unlikely. In turn, the occurrence of simpler forms of self-determination remains a controversial issue, in particular with respect to the case of self-organising dissipative systems. (shrink)

We develop a conceptual framework that connects biological heredity and organization. We refer to heredity as the cross-generation conservation of functional elements, defined as constraints subject to organizational closure. While hereditary objects are functional constituents of biological systems, any other entity that is stable across generations—and possibly involved in the recurrence of phenotypes—belongs to their environment. The central outcome of the organizational perspective consists in extending the scope of heredity beyond the genetic domain without merging it with the broad category (...) of cross-generation stability. After discussing some implications, we conclude with a reflection on the relationship between stability and variation. 1Introduction2From Extended Heredity to Cross-generation Stability 2.1Extending the scope of heredity: A brief state of the art2.2Rethinking heredity: Conceptual challenges3Biological Heredity in Light of Organization 3.1Biological organization within organisms and beyond3.2Extending organization in time3.3What is biological heredity?4Implications and Objections 4.1Heredity as a specific kind of cross-generation stability4.2Heredity at various levels of description4.3Non-functional and dysfunctional objects5Conclusions: From Conservation to Variation. (shrink)

In this paper, we advocate the idea that an adequate explanation of biological systems requires appealing to organizational closure as an emergent causal regime. We first develop a theoretical justification of emergence in terms of relatedness, by arguing that configurations, because of the relatedness among their constituents, possess ontologically irreducible properties, providing them with distinctive causal powers. We then focus on those emergent causal powers exerted as constraints, and we claim that biological systems crucially differ from other natural systems in (...) that they realize a closure of constraints, i.e. a second-order emergent regime of causation such that the constituents, each of them acting as a constraint, realize a mutual dependence among them, and are collectively able to self-maintain. Lastly, we claim that closure can be justifiably taken as an emergent regime of causation, without admitting that it inherently involves whole-parts causation, which would require to commit to stronger ontological and epistemological assumptions. (shrink)

Entry of the Encyclopedia of Systems Biology.

In Mossio & Taraborelli (2008) we challenged the assumption according to which the ecological and sensorimotor approaches are mere conceptual variations on the same enactive theme. We showed, on the contrary, that they endorse substantially different notions of an 'action-dependent perceptual invariant' and we submitted that this distinction has interesting theoretical and empirical implications. This dissimilarity between ecological and sensorimotor theories stems, in our view, from a more fundamental divergence on the nature of perceptual information. Since Gibson's work, the (...) ecological approach has adopted a fundamentally realist stance, according to which this information is 'picked up', 'revealed', 'encountered' and 'exploited' by the organism (as a range of affordances) but not 'constituted' by the activity of the organism. In contrast, sensorimotor approaches take an explicit interactivist position, which sees the perceiver's motor activity as a determinant of perceptual information itself. Pascal & O'Regan (2008) suggest that our analysis of the relationship between ecological, sensorimotor and enactive theories would benefit from a further distinction. The original enactive approach (Varela et al. 1991; Maturana, 2002; Thompson, 2007), they argue, should not be lumped together with contemporary sensorimotor approaches to perception: whereas sensorimotor theories endorse an externalist view of perception, according to which 'perception can only be understood as a form of interaction of the organism with the environment', the original enactive approach by Varela and collaborators would have strong 'idealist underpinnings'. (shrink)

Since Darwin, Biology has been framed on the idea of evolution by natural selection, which has profoundly influenced the scientific and philosophical comprehension of biological phenomena and of our place in Nature. This book argues that contemporary biology should progress towards and revolve around an even more fundamental idea, that of autonomy. Biological autonomy describes living organisms as organised systems, which are able to self-produce and self-maintain as integrated entities, to establish their own goals and norms, and to promote the (...) conditions of their existence through their interactions with the environment. Topics covered in this book include organisation and biological emergence, organisms, agency, levels of autonomy, cognition, and a look at the historical dimension of autonomy. The current development of scientific investigations on autonomous organisation calls for a theoretical and philosophical analysis. This can contribute to the elaboration of an original understanding of life - including human life - on Earth, opening new perspectives and enabling fecund interactions with other existing theories and approaches. This book takes up the challenge. (shrink)

The organizational account of biological functions interprets functions as contributions of a trait to the maintenance of the organization that, in turn, maintains the trait. As has been recently argued, however, the account seems unable to provide a unified grounding for both intra- and cross-generation functions, since the latter do not contribute to the maintenance of the same organization which produces them. To face this ‘ontological problem’, a splitting account has been proposed, according to which the two kinds of functions (...) require distinct organizational definitions. In this article, we propose a solution for the ontological problem, by arguing that intra- and cross-generation functions can be said to contribute in the same way to the maintenance of the biological organization, characterized in terms of organizational self-maintenance. As a consequence, we suggest maintaining a unified organizational account of biological functions. (shrink)

We characterize Hegel’s stance on biological purposiveness as consisting in a twofold move, which conceives organisms as intrinsically purposive natural systems and focuses on their behavioral and cognitive abilities. We submit that a Hegelian stance is at play in enactivism, the branch of the contemporary theory of biological autonomy devoted to the study of cognition and the mind. What is at stake in the Hegelian stance is the elaboration of a naturalized, although non-reductive, understanding of natural purposiveness.

The theory of biological autonomy provides a naturalized characterization of agency, understood as a general biological phenomenon that extends beyond the domain of intentionality and causation by mental states. Agency refers to the capacity of autonomous living beings (roughly speaking: organisms) to purposively and functionally control the interactions with the environment, and to adaptively modulate their own self-determining organization and behavior so as to maintain their own existence, construed as their intrinsic telos. We mention some crucial strengths of the autonomist (...) conception of agency, and some interesting challenges that it faces. Among the latter, we focus on the intertwined relationships between agency and evolution, as well as on the transition between agency and cognition. (shrink)

The Genotype-Phenotype (G-P) distinction was proposed in the context of Mendelian genetics, in the wake of late 19th century studies about heredity. In this paper, we provide a conceptual analysis that highlights that the G-P distinction was grounded on three pillars: observability, transmissibility, and causality. Originally, the genotype is the non-observable and transmissible cause of the phenotype, which is its observable and non-transmissible effect. We argue that the current developments of biology have called the validity of such pillars into question. (...) First, molecular biology has unveiled the putative material substrate of the genotype (qua DNA), making it an observable object. Second, numerous findings on nongenetic heredity suggest that some phenotypic traits can be directly transmitted. Third, recent organicist approaches to biological phenomena have emphasized the reciprocal causality between parts of a biological system, which notably applies to the relations between genotypes and phenotypes. As a consequence, we submit that the G-P distinction has lost its general validity, although it can still apply to specific situations. This calls for forging new frameworks and concepts to better describe heredity and development. (shrink)

For most of the twentieth century, biology forgot or largely neglected organization. By this term, I mean a certain mode of interaction among the parts of a system, which is by hypothesis distinctively realized by biological systems. While a systemic trend is progressively pervading various biological fields – notably Evolutionary Biology, Systems Biology and Origins of Life – I suggest that organization still remains a blind spot of biological thinking. Therefore, I submit, biology should be enriched by an explicit and (...) specific notion of organization, drawing in particular on the theory of autonomy, of which I recall some central tenets. I conclude with a brief overview of the scientific and philosophical tradition which has explicitly elaborated on biological organization, and of the more recent literature to which this book aims to contribute. (shrink)

We reply to Artiga and Martinez’s claim according to which the organizational account of cross-generation functions implies a backward looking interpretation of etiology, just as standard etiological theories of function do. We argue that Artiga and Martinez’s claim stems from a fundamental misunderstanding about the notion of “closure”, on which the organizational account relies. In particular, they incorrectly assume that the system, which is relevant for ascribing cross-generation organizational function, is the lineage. In contrast, we recall that organizational closure refers (...) to a relational description of a network of mutual dependencies, abstracted from time, in which production relations are irrelevant. From an organizational perspective, ascribing a function to an entity means locating it in the abstract system that realizes closure. In particular, the position of each entity within the relational system conveys an etiological explanation of its existence, because of its dependence on the effects exerted by other entities subject to closure. Because of the abstract relational nature of closure, we maintain that the organizational account of functions does not endorse a backward looking interpretation of etiology. As a consequence, it does not fall prey of epiphenomenalism. (shrink)

Biological regulation is what allows an organism to handle the effects of a perturbation, modulating its own constitutive dynamics in response to particular changes in internal and external conditions. With the central focus of analysis on the case of minimal living systems, we argue that regulation consists in a specific form of second-order control, exerted over the core regime of production and maintenance of the components that actually put together the organism. The main argument is that regulation requires a distinctive (...) architecture of functional relationships, and specifically the action of a dedicated subsystem whose activity is dynamically decoupled from that of the constitutive regime. We distinguish between two major ways in which control mechanisms contribute to the maintenance of a biological organisation in response to internal and external perturbations: dynamic stability and regulation. Based on this distinction an explicit definition and a set of organisational requirements for regulation are provided, and thoroughly illustrated through the examples of bacterial chemotaxis and the lac-operon. The analysis enables us to mark out the differences between regulation and closely related concepts such as feedback, robustness and homeostasis. (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)

Most of current theoretical analyses on biological functions can be classified as etiological or dispositional, depending on how they deal with the teleological dimension. In this paper, we propose a critical survey of these two perspectives, and we argue that some recent studies have set the basis of a new approach which grounds the teleological dimension of functional attributions in the organizational properties of living systems. We outline a new proposal within this new approach, based on an interpretation of living (...) systems as organized self-maintaining systems. (shrink)

Review of Alvaro Moreno and Matteo Mossio. 2015. Biological autonomy: a philosophical and theoretical enquiry.

The essay review summarizes the intention as well as some of the major topics from the book of A. Moreno and M. Mossio and discusses them against the background of recent considerations on the general understanding of organisms. The authors see themselves in the organicist tradition in biology and propose that a new understanding of living beings can be developed around the notion of organismic autonomy, which enables biological systems to maintain themselves in an environment through directed behavior.

The notion of subject matter is a key concern of contemporary philosophy of language and logic. A central task for a theory of subject matter is to characterise the notion of sentential subject matter, that is, to assign to each sentence of a given language a subject matter that may count as its subject matter. In this paper, we elaborate upon David Lewis’ account of subject matter. Lewis’ proposal is simple and elegant but lacks a satisfactory characterisation of sentential subject (...) matter. Drawing on linguistic literature on focus and on the question under discussion, we offer a neo-Lewisian account of subject matter, which retains all the virtues of Lewis’ but also includes an attractive characterisation of sentential subject matter. (shrink)

This paper defends a relational view of time based on recent work on quantum gravity. Julian barbour's relational approach to physical theory, in particular, is developed as a basis for a relational, rather than anti-realist, metaphysics of time.

The present paper discusses different approaches to metaphysics and defends a specific, non-deflationary approach that nevertheless qualifies as scientifically-grounded and, consequently, as acceptable from the naturalistic viewpoint. By critically assessing some recent work on science and metaphysics, we argue that such a sophisticated form of naturalism, which preserves the autonomy of metaphysics as an a priori enterprise yet pays due attention to the indications coming from our best science, is not only workable but recommended.

We put forward a new, ‘coherentist’ account of quantum entanglement, according to which entangled systems are characterized by symmetric relations of ontological dependence among the component particles. We compare this coherentist viewpoint with the two most popular alternatives currently on offer—structuralism and holism—and argue that it is essentially different from, and preferable to, both. In the course of this article, we point out how coherentism might be extended beyond the case of entanglement and further articulated.

We study the EPR-type correlations from the perspective of the relational interpretation of quantum mechanics. We argue that these correlations do not entail any form of “non-locality”, when viewed in the context of this interpretation. The abandonment of strict Einstein realism implied by the relational stance permits to reconcile quantum mechanics, completeness, (operationally defined) separability, and locality.

This paper investigates the reception and discussion of Jakob von Uexküll’s biological theory by two German thinkers of his time, Helmuth Plessner and Kurt Goldstein. It demonstrates how their bio-philosophical perspectives are on the one hand indebted to Uexküll’s theory and, on the other, critical of its tendency to excessively harmonize the relationship between living beings and their environment. This original critical reading of the _Umweltlehre_ is rooted in ambiguities within Uexküll’s own thought - between a dynamic conception of the (...) organism-environment relationship and the idea of "conformity to a plan" -,, which is here examined in the second section. In the third and fourth sections we will then focus on Plessner and Goldstein respectively, demonstrating how for these two authors the harmony between organism and environment is not an original state, but only reveals itself against the background of a tension; as such, it can only be partial, unstable and always changing. The two thinkers avoid the rigid alternative between Darwin’s concept of adaptation (_Anpassung_) and Uexküll’s “fitting into” (_Einpassung_) by theorizing the ideal state of the relationship between organism and environment in terms of “adequacy” (_Adäquatheit_) and “adaptability” (_Adaptiertheit_). Between organism and environment there is neither absolute separation nor perfect harmony, but rather a gap which can never be definitively fixed. (shrink)

As innovations in the field of vascular composite allotransplantation (VCA) progress, whole-eye transplantation (WET) is poised to transition from non-human mammalian models to living human recipients. Present treatment options for vision loss are generally considered suboptimal, and attendant concerns ranging from aesthetics and prosthesis maintenance to social stigma may be mitigated by WET. Potential benefits to WET recipients may also include partial vision restoration, psychosocial benefits related to identity and social integration, improvements in physical comfort and function, and reduced surgical (...) risk associated with a biologic eye compared to a prosthesis. Perioperative and postoperative risks of WET are expected to be comparable to those of facial transplantation (FT), and may be similarly mitigated by immunosuppressive protocols, adequate psychosocial support, and a thorough selection process for both the recipient and donor. To minimize the risks associated with immunosuppressive medications, the first attempts in human recipients will likely be performed in conjunction with a FT. If first-in-human attempts at combined FT-WET prove successful and the biologic eye survives, this opens the door for further advancement in the field of vision restoration by means of a viable surgical option. This analysis integrates recent innovations in WET research with the existing discourse on the ethics of surgical innovation and offers preliminary guidance to VCA programs considering undertaking WET in human recipients. (shrink)

This is the first part of a two-tier overview article on fundamentality in metaphysics and the philosophy of physics. It provides an introduction to the notion of fundamentality in metaphysics, as well as to several related concepts. The key issues in the contemporary debate on the topic are summarised, making systematic reference to the most relevant literature. In particular, various ways in which the fundamental entities and the fundamental structure of reality may be conceived are illustrated and discussed. A final (...) brief section looks at the methodological issue of naturalism, paving the way for the survey of fundamentality in the philosophy of physics, which is carried out in the second part. (shrink)

Boffa non-well-founded set theory allows for several distinct sets equal to their respective singletons, the so-called ‘Quine atoms’. Rieger contends that this theory cannot be a faithful description of set-theoretic reality. He argues that, even after granting that there are non-well-founded sets, ‘the extensional nature of sets’ precludes numerically distinct Quine atoms. In this paper we uncover important similarities between Rieger’s argument and how non-rigid structures are conceived within mathematical structuralism. This opens the way for an objection against Rieger, whilst (...) affording the theoretical resources for a defence of Boffa set theory as a faithful description of set-theoretic reality. (shrink)

The aim of this paper is twofold: first, I provide a cluster of theories of truth in classical logic that is (internally) consistent with global reflection principles: the theories of positive truth (and falsity). After that, I analyse the _epistemic value_ of such theories. I do so employing the framework of cognitive projects introduced by Wright (Proc Aristot Soc 78:167–245, 2004), and employed—in the context of theories of truth—by Fischer et al. (Noûs 2019. https://doi.org/10.1111/nous.12292 ). In particular, I will argue (...) that theories of positive truth are _trustworthy_, analogously to the theories of full disquotational truth. Moreover, I argue that, for a given cognitive project, _if_ the acceptance of trustworthy theories is taken to be an _epistemic norm_ of cognitive project, then one has good reasons to accept theories of positive truth over other rival theories of truth in classical logic. On the other hand, the latter theories are deemed epistemically unacceptable. (shrink)

Causal reductionism is the widespread assumption that there is no room for additional causes once we have accounted for all elementary mechanisms within a system. Due to its intuitive appeal, causal reductionism is prevalent in neuroscience: once all neurons have been caused to fire or not to fire, it seems that causally there is nothing left to be accounted for. Here, we argue that these reductionist intuitions are based on an implicit, unexamined notion of causation that conflates causation with prediction. (...) By means of a simple model organism, we demonstrate that causal reductionism cannot provide a complete and coherent account of ‘what caused what’. To that end, we outline an explicit, operational approach to analyzing causal structures. (shrink)