Idealization is a reasoning strategy that biologists use to describe, model and explain that purposefully departs from features known to be present in nature. Similar to other strategies of scientific reasoning, idealization combines distinctive strengths alongside of latent weaknesses. The study of ontogeny in model organisms is usually executed by establishing a set of normal stages for embryonic development, which enables researchers in different laboratory contexts to have standardized comparisons of experimental results. Normal stages are a form of idealization because (...) they intentionally ignore known variation in development, including variation associated with phenotypic plasticity (e.g. via strict control of environmental variables). This is a tension between the phenomenon of plasticity and the practice of staging that has consequences for evolutionary developmental investigation because variation is conceptually removed as a part of rendering model organisms experimentally tractable. Two compensatory tactics for mitigating these consequences are discussed: employing a diversity of model organisms and adopting alternative periodizations. (shrink)

The concept of agency is of crucial importance in cognitive science and artificial intelligence, and it is often used as an intuitive and rather uncontroversial term, in contrast to more abstract and theoretically heavy-weighted terms like “intentionality”, “rationality” or “mind”. However, most of the available definitions of agency are either too loose or unspecific to allow for a progressive scientific program. They implicitly and unproblematically assume the features that characterize agents, thus obscuring the full potential and challenge of modeling agency. (...) We identify three conditions that a system must meet in order to be considered as a genuine agent: a) a system must define its own individuality, b) it must be the active source of activity in its environment (interactionalasymmetry) and c) it must regulate this activity in relation to certain norms (normativity). We find that even minimal forms of proto-celular systems can already provide a paradigmatic example of genuine agency. By abstracting away some specific details of minimal models of living agency we define the kind of organization that is capable to meet the required conditions for agency (which is not restricted to living organisms). On this basis, we define agency as an autonomous organization that adaptively regulates its coupling with its environment and contributes to sustaining itself as a consequence. We find that spatiality and temporality are the two fundamental domains in which agency spans at different scales. We conclude by giving an outlook to the road that lies ahead in the pursuit to understand, model and synthesis agents. (shrink)

In addressing phenotypic evolution, this article reconsiders natural selection, random drift, developmental constraints, and internal selection in the new extended context of evolutionary developmental biology. The change of perspective from the "evolution of phenotypes" toward an "evolution of ontogenies" (evo-devo perspective) affects the reciprocal relationships among these different processes. Random drift and natural selection are sibling processes: two forms of post-productional sorting among alternative developmental trajectories, the former random, the latter nonrandom. Developmental constraint is a compound concept; it contains even (...) some forms of natural ("external" and "internal") selection. A narrower definition ("reproductive constraints") is proposed. Internal selection is not a selection caused by an internal agent. It is a form of environment-independent selection depending on the level of the organism's internal developmental or functional coordination. Selection and constraints are the main deterministic processes in phenotypic evolution but they are not opposing forces. Indeed, they are continuously interacting processes of evolutionary change, but with different roles that should not be confused. (shrink)

In this article, we propose some fundamental requirements for the appearance of adaptivity. We argue that a basic metabolic organization, taken in its minimal sense, may provide the conceptual framework for naturalizing the origin of teleology and normative functionality as it appears in living systems. However, adaptivity also requires the emergence of a regulatory subsystem, which implies a certain form of dynamic decoupling within a globally integrated, autonomous system. Thus, we analyze several forms of minimal adaptivity, including the special case (...) of motility. We go on to explain how an open-ended complexity growth of motility-based adaptive agency, namely, behavior, requires the appearance of the nervous system. Finally, we discuss some implications of these ideas for embodied robotics. (shrink)

Michael Ghiselin and David Hull’s individuality thesis is that biological species are individuals. Philosophers often treat the term “individual” as synonymous with “mereological sum” and characterize it in terms of mereology. It is easy to see how the biological project has been interpreted as a mereological one. This chapter argues that this is a mistake, that biological part/whole relations often violate the axioms of mereology. Conflating these projects confuses the central issues at stake in both, and makes the job of (...) evaluating either unnecessarily burdensome. Clarifying this helps identify the genuine metaphysical implications of the individuality thesis, which serves as an exemplar of scientifically informed metaphysics. (shrink)

Emergence seems necessary for any naturalistic account of the world — none of our familiar world existed at the time of the Big Bang, and it does now — and normative emergence is necessary for any naturalistic account of biology and mind — mental phenomena, such as representation, learning, rationality, and so on, are normative. But Jaegwon Kim’s argument appears to render causally efficacious emergence impossible, and Hume’s argument appears to render normative emergence impossible, and, in its general form, it (...) precludes any emergence at all. I argue that both of these barriers can be overcome, and, in fact, that they each constitute reductios of their respective underlying presuppositions. In particular, causally efficacious ontological emergence can be modeled, but only within a process metaphysics, thus avoiding Kim’s argument, and by making use of non-abbreviatory forms of definition, thus avoiding Hume’s argument. I illustrate these points with models of the emergent nature of normative function and of representation. (shrink)

In the early 1920s, Hans Reichenbach and Kurt Lewin presented two topological accounts of time that appear to be interrelated in more than one respect. Despite their different approaches, their underlying idea is that time order is derived from specific structural properties of the world. In both works, moreover, the notion of genidentity--i.e., identity through or over time--plays a crucial role. Although it is well known that Reichenbach borrowed this notion from Kurt Lewin, not much has been written about their (...) relationship, nor about the way Lewin implemented this notion in his own work in order to ground his topology. This paper examines these two early versions of the topology of time, and follows the extent of Lewin’s influence on Reichenbach’s proposal. (shrink)

We can learn much about perceptual experience by thinking about how it can mislead us. In this paper, I explore whether, and how, olfactory experience can mislead. I argue that, in the case of olfactory experience, the traditional distinction between illusion and hallucination does not apply. Integral to the traditional distinction is a notion of ‘object-failure’—the failure of an experience to present objects accurately. I argue that there are no such presented objects in olfactory experience. As a result, olfactory experience (...) can only mislead by means of a kind of property hallucination. The implications of my arguments are twofold. First, we see that accounts of representational content cannot always be based on the visual model. And, secondly, we see that we must recast the notion of nonveridicality, allowing for a notion of non-veridical experience that is disengaged from any particular object. (shrink)

We propose a modular ontology of the dynamic features of reality. This amounts, on the one hand, to a purely spatial ontology supporting snapshot views of the world at successive instants of time and, on the other hand, to a purely spatiotemporal ontology of change and process. We argue that dynamic spatial ontology must combine these two distinct types of inventory of the entities and relationships in reality, and we provide characterizations of spatiotemporal reasoning in the light of the interconnections (...) between them. (shrink)

This chapter introduces the main issues and themes of the volume. Approaches to individuality from metaphysics and philosophy of science are contrasted. Recent philosophical developments regarding concepts of biological and physical individuality are exposed. These research trends show how philosophy of physics and philosophy of biology address differently the question of what an individual is. Five main divergences are identified: the centrality of part-whole questions, the issue of identical individuals, the importance of the Principle of the Identity of Indiscernibles and, (...) finally, the importance of structuralist concerns. At the end of the chapter, the structure of the book is explained in detail. (shrink)

The paper contains a novel realist account of causal production and the necessary connection between cause and effect. I argue that the asymmetric relation between causally connected events must be regarded as a product of a symmetric interaction between two or more entities. All the entities involved contribute to the producing, and so count as parts of the cause, and they all suffer a change, and so count as parts of the effect. Cause and effect, on this account, are two (...) different states of the very same compound substance, or system, one coming to exist out of the other. (shrink)

Substance ontologists claim that substances are ontologically primary because the category of substance enjoys unique explanatory potential. Unless it can be shown that "only" substances fulfill the central explanatory tasks in ontology, this inference from explanatory success to ontological primacy amounts to a fallacy akin to the error Whitehead called 'the fallacy of misplaced concreteness'. I investigate recent prototypical arguments for substance metaphysics and try to show that some explanatory functions of substance can also be fulfilled by other ontological categories. (...) In particular, I argue against M. Ayers that there is no reason to think that all and only substances are discrete individuals, natural wholes, and logical units. I conclude that the category of substance does not provide us with a uniquely powerful explanans for the notion of logical and physical unity. (shrink)

Both natural and engineered systems are fundamentally dynamical in nature: their defining properties are causal, and their functional capacities are causally grounded. Among dynamical systems, an interesting and important sub-class are those that are autonomous, anticipative and adaptive (AAA). Living systems, intelligent systems, sophisticated robots and social systems belong to this class, and the use of these terms has recently spread rapidly through the scientific literature. Central to understanding these dynamical systems is their complicated organisation and their consequent capacities for (...) re- and self- organisation. But there is at present no general analysis of these capacities or of the requisite organisation involved. We define what distinguishes AAA systems from other kinds of systems by characterising their central properties in a dynamically interpreted information theory. (shrink)

The concept of genidentity has been proposed as a way to better understand identity through time, especially in physics and biology. The genidentity view is utterly anti-substantialist in so far as it suggests that the identity of X through time does not presuppose whatsoever the existence of a permanent “core” or “substrate” of X. Yet applications of this concept to real science have been scarce and unsatisfying. In this paper, our aim is to show that a well-defined concept of functional (...) genidentity can be crucial to shed light on identity through time in classical physics and especially in biology. Finally, we show that understanding identity on the basis of continuity suggests a move towards an ontology of processes. (shrink)

The aim of this paper is to address a longstanding concern about the linguistic ‘relativ- ity’ of ontological categories, and resulting limitations in the scope of ontological theo- ries. Given recent evidence on the influence of language on cognitive dispositions, do we have empirical reasons to doubt that there are ontological categories that have uni- versal scope across languages? I argue that this is the case, at least if we retain the stan- dard ‘inferential’ approach within analytical ontology, i.e., if (...) we evaluate ontological interpretations of L-sentences relative to certain material inferences in L. Research in linguistic typology suggests that types of entities postulated for the domain of Indo- European languages cannot capture the ontological commitments of the (much larger group of) non-Indo-European languages. Ontological category theory thus seems to have three options. The first option is to abandon the standard ‘inferential’ approach to ontological category theory. Alternatively, if we stay with the inferential approach, we face the following choice. Either ontology must let go of its ambitions to provide general domain descriptions for any language and settle for the more modest project of reconstructing the ontological commitments of a group of natural languages. Or else analytical ontologists should turn to linguistic typology in order to accommodate the diversity of inferential structures embedded in natural languages. I recommend and ex- plore this third option, illustrating a strategy for how to construct a domain theory that can be used across languages. In a first step I show how linguistic research on the se- mantics of verbs and nouns (studies on so-called “Aktionsarten” and “Seinsarten”) can be used to identify the inferential patterns of ten basic concepts of modes of existence in time and space. In a second step I show how these inferential data can be inter- preted ontologically within General Process Theory, an ontological framework based on nonparticular individuals (“dynamics”). -/- . (shrink)

The paper argues against the central dogma and its interpretation by C. Kenneth Waters and Alex Rosenberg. I argue that certain phenomena in the regulation of gene expression provide a break with the central dogma, according to which sequence specificity for a gene product must be template derived. My thesis of 'molecular epigenesis' with its three classes of phenomena, sequence 'activation', 'selection', and 'creation', is exemplified by processes such as transcriptional activation, alternative cis- and trans-splicing, and RNA editing. It argues (...) that other molecular resources share the causal role of genes; the sequence specificity for the linear sequence of any gene product is distributed between the coding sequence, cis-acting sequences, trans-acting factors, environmental signals, and the contingent history of the cell (thesis of distributed causal specificity). I conclude that the central dogma has unnecessarily restricted genetic research to the sequencing of protein-coding genes, unilinear pathway analyses, and the focus on exclusive specificity. (shrink)

Neurobiology studies mechanisms of cell signalling. A key question is how cells recognise specific signals. In this context, olfaction has become an important experimental system over the past 25 years. The olfactory system responds to an array of structurally diverse stimuli. The discovery of the olfactory receptors (ORs), recognising these stimuli, established the olfactory pathway as part of a greater group of signalling mechanisms mediated by G-protein-coupled receptors (GPCRs). GPCRs are the largest protein family in the mammalian genome and involved (...) in numerous fundamental physiological processes. The OR family exhibits two characteristics that make them an excellent model system to understand GPCRs: its size and the structural diversity of its members. Research on the OR binding site investigates what amino acid sequences determine the receptor-binding capacity. This promises a better understanding of how the basic genetic makeup of GPCRs relates to their diversification in ligand-binding capacities. (shrink)