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)

There is a growing consensus among philosophers of science that scientific endeavors of understanding the human mind or the brain exhibit explanatory pluralism. Relatedly, several philosophers have in recent years defended an interventionist approach to causation that leads to a kind of causal pluralism. In this paper, I explore the consequences of these recent developments in philosophy of science for some of the central debates in philosophy of mind. First, I argue that if we adopt explanatory pluralism and the interventionist (...) approach to causation, our understanding of physicalism has to change, and this leads to what I call pluralistic physicalism. Secondly, I show that this pluralistic physicalism is not endangered by the causal exclusion argument. (shrink)

Although scientific realism is the default position in the life sciences, philosophical accounts of realism are geared towards physics and run into trouble when applied to fields such as biology or neuroscience. In this paper, I formulate a new robustness-based version of entity realism, and show that it provides a plausible account of realism for the life sciences that is also continuous with scientific practice. It is based on the idea that if there are several independent ways of measuring, detecting (...) or deriving something, then we are justified in believing that it is real. I also consider several possible objections to robustness-based entity realism, discuss its relationship to ontic structural realism, and show how it has the potential to provide a novel response to the pessimistic induction argument. (shrink)

The relationship between psychological states and the brain remains an unresolved issue in philosophy of psychology. One appealing solution that has been influential both in science and in philosophy is Dennett’s concept of the intentional stance, according to which beliefs and desires are real and objective phenomena, but not necessarily states of the brain. A fundamental shortcoming of this approach is that it does not seem to leave any causal role for beliefs and desires in influencing behavior. In this paper, (...) I show that intentional states ascribed from the intentional stance should be seen as real causes, develop this to an independently plausible ontological position, and present a response to the latest interventionist causal exclusion worries. (shrink)

To identify and conceptualize research problems in science, philosophers and often scientists rely on classical accounts of problems that focus on intellectual problems defined in relation to theories. Recently, philosophers have begun to study the structures and functions of research problems not defined in relation to theories. Furthermore, scientists have long pursued research problems often labeled as practical or applied. As yet, no account of problems specifies the description of both so-called intellectual problems and so-called applied problems. This article proposes (...) a new conceptual framework of problems that accounts both for intellectual aspects of problems and for their practical or applied aspects. I illustrate the account with an example of a recent research project from evolutionary biology, and I indicate further routes by that to develop the account, especially in connection to empirical studies of science. (shrink)

Researchers often pursue proof of concept research, but criteria for evaluating such research remain poorly specified. This article proposes a general framework for proof of concept research that k...

The aim of this paper is to offer an account of epistemic justification suitable for the context of theory pursuit, that is, for the context in which new scientific ideas, possibly incompatible with the already established theories, emerge and are pursued by scientists. We will frame our account paradigmatically on the basis of one of the influential systems of epistemic justification: Laurence Bonjour’s coherence theory of justification. The idea underlying our approach is to develop a set of criteria which indicate (...) that the pursued system is promising of contributing to the epistemic goal of robustness of scientific knowledge and of developing into a candidate for acceptance. In order to realize this we will (a) adjust the scope of Bonjour’s standards—consistency, inferential density, and explanatory power, and (b) complement them by the requirement of a programmatic character. In this way we allow for the evaluation of the “potential coherence” of the given epistemic system. (shrink)

In this article, I focus on the role of computer simulations as exploratory strategies. I begin by establishing the non-theory-driven nature of simulations. This refers to their ability to characterize phenomena without relying on a predefined conceptual framework that is provided by an implemented mathematical model. Drawing on Steinle’s notion of exploratory experimentation and Gelfert’s work on exploratory models, I present three exploratory strategies for computer simulations: (1) starting points and continuation of scientific inquiry, (2) varying the parameters, and (3) (...) scientific prototyping. (shrink)

Whether we live in a world of autonomous things, or a world of interconnected processes in constant flux, is an ancient philosophical debate. Modern biology provides decisive reasons for embracing the latter view. How does one understand the practices and outputs of science in such a dynamic, ever-changing world - and particularly in an emergency situation such as the COVID-19 pandemic, where scientific knowledge has been regarded as bedrock for decisive social interventions? We argue that key to answering this question (...) is to consider the role of the activity of reification within the research process. Reification consists in the identification of more or less stable features of the flux, and treating these as constituting stable things. As we illustrate with reference to biological and biomedical research on COVID-19, reification is a necessary component of any process of inquiry and comes in at least two forms: means reification, when researchers create objects meant to capture features of the world, or phenomena, in order to be able to study them; and target reification, when researchers infer an understanding of phenomena from an investigation of the epistemic objects created to study them. We note that both objects and phenomena are dynamic processes and argue that have no reason to assume that changes in objects and phenomena track one another. We conclude that failure to acknowledge these forms of reification and their epistemic role in scientific inquiry can have dire consequences for how the resulting knowledge is interpreted and used. (shrink)

I present a novel, collaborative, methodology for linguistics: what I call the ‘explanatory economy’. According to this picture, multiple models/theories are evaluated based on the extent to which they complement one another with respect to data coverage. I show how this model can resolve a long-standing worry about the methodology of generative linguistics: that by creating too much distance between data and theory, the empirical credentials of this research program are tarnished. I provide justifications of such methodologically central distinctions as (...) the competence/performance and core/periphery distinction, and then show how we can understand the push for simplicity in the history of generative grammar in this light. (shrink)

More and more researchers are examining grammar acquisition from theoretical perspectives that treat it as an emergent phenomenon. In this essay, I argue that a robustly developmental perspective provides a potential explanation for some of the well-known crosslinguistic features of early child language: the process of acquisition is shaped in part by the developmental constraints embodied in von Baer’s law of development. An established model of development, the Developmental Lock, captures and elucidates the probabilistic generalizations at the heart of von (...) Baer’s law. When this model is applied to the acquisition of grammar, it predicts that grammatical achievements that are more generatively entrenched will emerge earlier in development and will be more developmentally resilient than those that are less generatively entrenched. I show that the first prediction is supported by a wealth of psycholinguistic evidence involving typically developing children and that the second prediction is supported by numerous studies involving both children who receive deficient linguistic input and children who experience various language impairments. The success of this model demonstrates the analytic potential of a developmental approach to the study of language acquisition. (shrink)

Scientific realists argue that a good track record of multi-agent, and multiple method, validation of empirical claims is itself evidence that those claims, at least partially and approximately, reflect ways nature actually is independent of the ways we conceptualize it. Constructivists contend that successes in validating empirical claims only suffice to establish that our ways of modelling the world, our “constructions,” are useful and adequate for beings like us. This essay presents a thought experiment in which beings like us intersubjectively (...) validate claims about properties of particular things in nature under conditions in which those beings have profoundly different personal phenomenological experiences of those properties. I submit that the thought experiment scenario parallels our actual situation, and argue that this shows that successes in intersubjectively validating empirical claims are indeed enough to claim victory for the realist. More specifically, I champion a variation of realism that marries Ronald Giere’s brand of ‘perspectival realism’ with Philip Kitcher’s ‘real realism,’ and posits that causal relations between ourselves and properties instantiated in nature ground our references to the relevant properties even though our conceptions of them are perspective relative. (shrink)

Sagoff (2016) criticizes widely used “theoretical” methods in ecology; arguing that those methods employ models that rely on problematic metaphysical assumptions and are therefore uninformative and useless for practical decision-making. In this paper, I show that Sagoff misconstrues how such model-based methods work in practice, that the main threads of his argument are problematic, and that his substantive conclusions are consequently unfounded. Along the way, I illuminate several ways the model-based inferential methods he criticizes can be, and have been, usefully (...) informative. (shrink)

This essay extends my “invisible disagreement” argument for Color Realism (2017) to formulate an argument for Direct Realism. It uses a variation of an “inverted qualia” thought experiment to show that successes in intersubjectively validating empirical claims about colors is proof that a nuanced version of Direct Realism is correct.

The logic of genetic discovery has changed little over time, but the focus of biology is shifting from simple genotype–phenotype relationships to complex metabolic, physiological, developmental, and behavioral traits. In light of this, the traditional reductionist view of individual genes as privileged difference‐making causes of phenotypes is re‐examined. The scope and nature of genetic effects in complex regulatory systems, in which dynamics are driven by regulatory feedback and hierarchical interactions across levels of organization are considered. This review argues that it (...) is appropriate to treat genes as specific actual difference‐makers for the molecular regulation of gene expression. However, they are often neither stable, proportional, nor specific as causes of the overall dynamic behavior of regulatory networks. Dynamical models, properly formulated and validated, provide the tools to probe cause‐and‐effect relationships in complex biological systems, allowing to go beyond the limitations of genetic reductionism to gain an integrative understanding of the causal processes underlying complex phenotypes. (shrink)

Explanation in terms of gene regulatory networks has become standard practice in evolutionary developmental biology. In this paper, we argue that GRNs fail to provide a robust, mechanistic, and dynamic understanding of the developmental processes underlying the genotype–phenotype map. Explanations based on GRNs are limited by three main problems: the problem of genetic determinism, the problem of correspondence between network structure and function, and the problem of diachronicity, as in the unfolding of causal interactions over time. Overcoming these problems requires (...) dynamic mechanistic explanations, which rely not only on mechanistic decomposition, but also on dynamic modeling to reconstitute the causal chain of events underlying the process of development. We illustrate the power and potential of this type of explanation with a number of biological case studies that integrate empirical investigations with mathematical modeling and analysis. We conclude with general considerations on the relation between mechanism and process in evo-devo. (shrink)

As the debate about holism and reductionism in ecology has ebbed in the last twenty years, this article aims to reassess the traditional opposition between holistic and reductionist epistemologies during the development of population biology. The history of the notion of carrying capacity, the upper demographic limit of a viable population, will be analyzed as a paradigmatic case of the progressive imposition of reductionist strategies, from both an epistemological and a semantic point of view, since the middle of the twentieth (...) century. Then, Richard Looijen’s reduction of the carrying capacity concept to the niche partitioning theory will be assessed and rebuked for both empirical and logical reasons. Eventually, some recent “weak” and “hard” emergent conceptualizations of the notion of carrying capacity, in logistic map models or in coupled niche-population systems, will be presented in order to show how they call into question the nature and the use of the notion of carrying capacity as a predefined ecological limit. (shrink)

I begin to develop a framework for emergence in the physical sciences. Namely, I propose to explicate ontological emergence in terms of the notion of ‘novel reference’, and of an account of interpretation as a map from theory to world. I then construe ontological emergence as the “failure of the interpretation to mesh” with an appropriate linkage map between theories. Ontological emergence can obtain between theories that have the same extension but different intensions, and between theories that have both different (...) extensions and intensions. I illustrate the framework in three examples: the emergence of spontaneous magnetisation in a ferromagnet, the emergence of masslessness, and the emergence of space, in specific models of physics. The account explains why ontological emergence is independent of reduction: namely, because emergence is primarily concerned with adequate interpretation, while the sense of reduction that is relevant here is concerned with inter-theoretic relations between uninterpreted theories. (shrink)

I begin to develop a framework for emergence in the physical sciences. Namely, I propose to explicate ontological emergence in terms of the notion of ‘novel reference’, and of an account of interpretation as a map from theory to world. I then construe ontological emergence as the “failure of the interpretation to mesh” with an appropriate linkage map between theories. Ontological emergence can obtain between theories that have the same extension but different intensions, and between theories that have both different (...) extensions and intensions. I illustrate the framework in three examples: the emergence of spontaneous magnetisation in a ferromagnet, the emergence of masslessness, and the emergence of space, in specific models of physics. The account explains why ontological emergence is independent of reduction: namely, because emergence is primarily concerned with adequate interpretation, while the sense of reduction that is relevant here is concerned with inter-theoretic relations between uninterpreted theories. (shrink)

I begin to develop a framework for emergence in the physical sciences. Namely, I propose to explicate ontological emergence in terms of the notion of ‘novel reference’, and of an account of interpretation as a map from theory to world. I then construe ontological emergence as the “failure of the interpretation to mesh” with an appropriate linkage map between theories. Ontological emergence can obtain between theories that have the same extension but different intensions, and between theories that have both different (...) extensions and intensions. I illustrate the framework in three examples: the emergence of spontaneous magnetisation in a ferromagnet, the emergence of masslessness, and the emergence of space, in specific models of physics. The account explains why ontological emergence is independent of reduction: namely, because emergence is primarily concerned with adequate interpretation, while the sense of reduction that is relevant here is concerned with inter-theoretic relations between uninterpreted theories. (shrink)

We critique the organizational account of biological functions by showing how its basis in the closure of constraints fails to be objective. While the account treats constraints as objective features of physical systems, the number and relationship of potential constraints are subject to potentially arbitrary redescription by investigators. For example, we show that self-maintaining systems such as candle flames can realize closure on a more thorough analysis of the case, contradicting the claim that these “simple” systems lack functional organization. This (...) also raises problems for Moreno and Mossio’s associated theory of biological autonomy, which asserts that living beings are distinguished by their possession of a closed system of constraints that channel and regulate their metabolic processes. (shrink)

Paleobiologists often provide simple narratives to explain complex, contingent episodes. These narratives are sometimes ‘one-shot hypotheses’ which are treated as being mutually exclusive with other possible explanations of the target episode, and are thus extended to accommodate as much about the episode as possible. I argue that a provisional preference for such hypotheses provides two kinds of productive scaffolding. First, they generate ‘hypothetical difference-makers’: one-shot hypotheses highlight and isolate empirically tractable dependencies between variables. Second, investigations of hypothetical difference-makers provision explanatory (...) resources, the ‘raw materials’ for constructing more complex—and likely more adequate—explanations. Provisional preferences for simple, one-shot hypotheses in historical science, then, is defeasibly justified on indirect—strategic—grounds. My argument is made in reference to recent developments regarding the K–Pg extinction. (shrink)

Common philosophical accounts of creativity align creative products and processes with a particular kind of agency: namely, that deserving of praise or blame. Considering evolutionary examples, we explore two ways of denying that creativity requires forms of agency. First, we argue that decoupling creativity from praiseworthiness comes at little cost: accepting that evolutionary processes are non-agential, they nonetheless exhibit many of the same characteristics and value associated with creativity. Second, we develop a ‘product-first’ account of creativity by which a process (...) is creative just in case it gives rise to products deserving of certain forms of aesthetic engagement. (shrink)

Angela Potochnik’s Idealization and the Aims of Science defends an ambitious and systematic account of scientific knowledge: ultimately science pursues human understanding rather than truth. Potochnik argues that idealization is rampant and unchecked in science. Further, given that idealizations involve departures from truth, this suggests science is not primarily about truth. I explore the relationship between truths about causal patterns and scientific understanding in light of this, and suggest that Potochnik underestimates the importance and power of highly particular narrative explanations.

Angela Potochnik’s Idealization and the Aims of Science (Chicago) defends an ambitious and systematic account of scientific knowledge: ultimately science pursues human understanding rather than truth. Potochnik argues that idealization is rampant and unchecked in science. Further, given that idealizations involve departures from truth, this suggests science is not primarily about truth. I explore the relationship between truths about causal patterns and scientific understanding in light of this, and suggest that Potochnik underestimates the importance and power of highly particular narrative (...) explanations. (shrink)

A survey of contemporary philosophical and scientific literatures reveals that different authors employ the term ‘heuristic’ in ways that deviate from, and are sometimes inconsistent with, one another. Given its widespread use in philosophy and cognitive science generally, it is striking that there appears to be little concern for a clear account of what phenomena heuristics pick out or refer to. In response, I consider several accounts of ‘heuristic’, and I draw a number of distinctions between different sorts of heuristics (...) in order to make sense of various research programmes. I then develop a working characterization of ‘heuristic’ which is shown to be coherent and robust enough to serve as a kind within philosophy and cognitive science broadly. My intent is not to pursue a unified account of ‘heuristic’, but to highlight some features of certain kinds of heuristics that are important for theorizing about cognition in order to proceed with a science of the mind/brain. 1 Why We Need an Appropriate Characterization of ‘Heuristic’2 Inadequate Definitions2.1 A positive attempt2.2 Heuristics versus guaranteed correct outcomes3 A Taxonomy of Heuristics3.1 Stimulus-driven versus heuristic3.2 Perceptual versus cognitive heuristics3.3 Computational versus cognitive heuristics3.4 Methodological versus inferential heuristics3.5 Summary of distinctions4 Characterizing Cognitive Heuristics4.1 Heuristics as rules of thumb4.2 Beyond rules of thumb: exploiting information5 Concluding Remarks. (shrink)

A longstanding criticism of Ernest Nagel's model of reduction is that it fails to take theory change into account. This criticism builds on the received view that Nagelian reductions are incompatible with theory change. This article challenges the received view by showing that Nagel's model can easily accommodate theory change. Indeed, Nagel's model is essentially static as it only gives unchanging formal and nonformal conditions for reduction; in contrast, theory change belongs to the dynamic history of science; as a result, (...) the application of Nagel's model to scientific knowledge from different historical periods yields a series of Nagelian reductions of different degrees of reductive success. This Nagelian treatment of theory change is illustrated by considering the enterprise of reducing thermodynamics to statistical mechanics in the late nineteenth century. It is also contended that, in handling theory change Nagel's model has greater merits than subsequent models (exemplified by Kenneth Schaffner's general reduction-replacement model). This article concludes by suggesting that Nagel's model of reduction deals with theory change exactly in the same way as logical empiricism does with historicism. (shrink)

In the past half century, the theory of the firm has become a specific and prolific research field. However, the social ontology of this central institution of capitalism has never truly been the subject of investigation. I consider this negligence harmful for organizational economics and management and, more broadly, for the social sciences, notably because the first and central question raised by the theory of the firm relates to its nature: What is a firm? For this reason, I propose some (...) novel considerations for a social ontology of the firm by focusing on social emergence, reconstitution, the two-level institutional logic of the firm, complex organizational dynamics and interacting mechanisms, and power. (shrink)

This paper defends the viability of de-idealization strategies in economic modeling against recent criticism. De-idealization occurs when an idealized assumption of a theoretical model is replaced with a more realistic one. Recently, some scholars have raised objections against the possibility or fruitfulness of de-idealizing economic models, suggesting that economists do not employ this kind of strategy. We present a detailed case study from the theory of industrial organization, discussing three different models, two of which can be construed as de-idealized versions (...) of the first (the so-called Bertrand model of oligopoly). We conclude that recent pessimism about de-idealization in economics is largely unfounded, and that de-idealization strategies are not only possible but also widely employed in economics. (shrink)

Gebharter has proposed using one of the best known Bayesian network causal discovery algorithms, PC, to identify the constitutive dependencies underwriting mechanistic explanations. His proposal assumes that mechanistic constitution behaves like deterministic direct causation, such that PC is directly applicable to mixed variable sets featuring both causal and constitutive dependencies. Gebharter claims that such mixed sets, under certain restrictions, comply with PC’s background assumptions. The aim of this article is to show that Gebharter’s proposal incurs severe problems, ultimately rooted in (...) the widespread non-compliance of mechanistic systems with PC’s assumptions. This casts severe doubts on the attempt to implicitly define constitution as a form of deterministic direct causation complying with PC’s assumptions. (shrink)

Glennan appeals to interventions to solve the ontological and explanatory regresses that threaten his mechanistic account of causality . I argue that Glennan’s manoeuvre fails. The appeal to interventions is not able to address the ontological regress, and it blocks the explanatory regress only at the cost of making the account inapplicable to non-modular mechanisms. I offer a solution to the explanatory regress that makes use of dynamic Bayesian networks. My argument is illustrated by a case study from systems biology, (...) namely, the mechanism for the irreversibility of apoptosis. I conclude by pointing out the implications of my argument for Glennan’s mechanistic account of causality and, more generally, for accounts of mechanistic explanation based on interventions. 1 Introduction2 Glennan’s Account of Causality3 Objections to Glennan’s Account4 Glennan’s Replies5 Ontological Symmetry?6 Explanatory Symmetry?7 A Solution to the Explanatory Regress8 The Prospects of Glennan’s Account. (shrink)

Although “theory” has been the prevalent unit of analysis in the meta-study of science throughout most of the twentieth century, the concept remains elusive. I further explore the leitmotiv of several authors in this issue: that we should deal with theorizing (rather than theory) in biology as a cognitive activity that is to be investigated naturalistically. I first contrast how philosophers and biologists have tended to think about theory in the last century or so, and consider recent calls to upgrade (...) the role of theory in the life sciences against the background of the recent “data deluge” in molecular biology, systems biology, etc. I then review thinking about theory in biology in relation to physical theory as a positive or negative exemplar. I conclude by discussing various aspects of a positive program for “naturalizing theorizing.”. (shrink)

Biologists frequently draw on ideas and terminology from engineering. Evolutionary systems biology—with its circuits, switches, and signal processing—is no exception. In parallel with the frequent links drawn between biology and engineering, there is ongoing criticism against this cross-fertilization, using the argument that over-simplistic metaphors from engineering are likely to mislead us as engineering is fundamentally different from biology. In this article, we clarify and reconfigure the link between biology and engineering, presenting it in a more favorable light. We do so (...) by, first, arguing that critics operate with a narrow and incorrect notion of how engineering actually works, and of what the reliance on ideas from engineering entails. Second, we diagnose and diffuse one significant source of concern about appeals to engineering, namely that they are inherently and problematically metaphorical. We suggest that there is plenty of fertile ground left for a continued, healthy relationship between engineering and biology. (shrink)

Human “free will” has been made problematic by several recent arguments against mental causation, the unity of the I or “self,” and the possibility that conscious decision-making could be temporally prior to action. This paper suggests a pathway through this thicket for free will or self-determination. Doing so requires an account of mind as an emergent process in the context of animal psychology and mental causation. Consciousness, a palpable but theoretically more obscure property of some minds, is likely to derive (...) from complex animals’ real-time monitoring of internal state in relation to environment. Following Antonio Damasio, human mind appears to add to nonhuman “core consciousness” an additional narrative “self-consciousness.” The neurological argument against free will, most famously from Benjamin Libet, can be avoided as long as “free will” means, not an impossible event devoid of prior causation, but an occasional causal role played by narrative self-consciousness in behavioral determination. There is no necessary incompatibility between the scientific and evolutionary exploration of mind and consciousness and the uniquely self-determining capabilities of human mentality which are based on the former. (shrink)

Robert Brandom's book Between Saying and Doing: Towards an Analytic Pragmatism does not incorporate the larger views of any of the “pragmatisms” he deliberately invokes, such as those of the classical American pragmatists, apart from an “analytic” cohort of Wittgenstein-inspired pragmatisms that he himself favors.

Is Joseph Margolis a member of the often neglected school of “Columbia naturalism”? Columbia naturalism promoted a distinctive non-reductive nationalism in mid-twentieth-century America. Inspired by pragmatism, and Dewey in particular, its members included Ernest Nagel, John Herman Randall, Joseph Blau, Herbert Schneider, and Justus Buchler. Margolis received his degree from Columbia in 1953. Neither his early work in aesthetics nor his mature attempt to justify pragmatic themes in an uncompromising dialogue with analytic and continental philosophy seems particularly “Columbian.” Neither does (...) his radical endorsement of a kind of relativism. However, Margolis is after all some kind of naturalist. Furthermore, the Columbians shared a forgotten doctrine, called “objective relativism.” If the combination of naturalism and relativism is a Columbian fruit, Margolis may have has fallen closer to the tree than first appears. (shrink)

ABSTRACT I propose a division of the literature on natural kinds into metaphysical worries, semantic worries, and methodological worries. I argue that the latter set of worries, which concern how classification influences scientific practices, should occupy centre stage in philosophy of science discussions about natural kinds. I apply this methodological framework to the problems of classifying chemical species and nanomaterials. I show that classification in nanoscience differs from classification in chemistry because the latter relies heavily on compositional identity, whereas the (...) former must consider additional properties, namely, size, shape, and surface chemistry. I use this difference to argue for a scale-dependent theory of scientific classification. _1_ Introduction _2_ The Methodological Problem of Kinds _3_ Chemical Kindhood: Reactivity, Microstructure, and the Structure–Property Paradigm _4_ Scale-Dependence and Nanoscale Kinds _5_ Conclusion. (shrink)

One of the biggest problems in applications of animal welfare science is our ability to make comparisons between different individuals, both within and across species. Although welfare science provides methods for measuring the welfare of individual animals, there’s no established method for comparing measures between individuals. In this paper I diagnose this problem as one of underdetermination—there are multiple conclusions given the data, arising from two sources of variation that we cannot distinguish: variation in the underlying target variable (welfare experience) (...) and in the relationship of measured indicators to the target. I then describe some of the possible methods of making comparisons, based on the use of similarity assumptions that will have greater or lesser justification in different circumstances, and the alternative methods we may use when direct comparisons are not possible. In the end, all our available options for making welfare comparisons are imperfect, and we need to make explicit context-specific decisions about which will be best for the task at hand while acknowledging their potential limitations. Future developments in our understanding of the biology of sentience will help strengthen our methods of making comparisons. (shrink)

This paper addresses what we consider to be the most pressing challenge for the emerging science of consciousness: the measurement problem of consciousness. That is, by what methods can we determine the presence of and properties of consciousness? Most methods are currently developed through evaluation of the presence of consciousness in humans and here we argue that there are particular problems in application of these methods to nonhuman cases—what we call the indicator validity problem and the extrapolation problem. The first (...) is a problem with the application of indicators developed using the differences between conscious and unconscious processing in humans to the identification of other conscious vs. nonconscious organisms or systems. The second is a problem in extrapolating any indicators developed in humans or other organisms to artificial systems. However, while pressing ethical concerns add urgency to the attribution of consciousness and its attendant moral status to nonhuman animals and intelligent machines, we cannot wait for certainty and we advocate the use of a precautionary principle to avoid causing unintentional harm. We also intend that the considerations and limitations discussed in this paper can be used to further analyze and refine the methods of consciousness science with the hope that one day we may be able to solve the measurement problem of consciousness. (shrink)

Traditional accounts of the role of learning in evolution have concentrated upon its capacity as a source of fitness to individuals. In this paper I use a case study from invasive species biology—the role of conditioned taste aversion in mitigating the impact of cane toads on the native species of Northern Australia—to highlight a role for learning beyond this—as a source of evolvability to populations. This has two benefits. First, it highlights an otherwise under-appreciated role for learning in evolution that (...) does not rely on social learning as an inheritance channel nor “special” evolutionary processes such as genetic accommodation (both of which many are skeptical about). Second, and more significantly, it makes clear important and interesting parallels between learning and exploratory behaviour in development. These parallels motivate the applicability of results from existing research into learning and learning evolution to our understanding of the evolution of evolvability more generally. (shrink)

Despite its pervasiveness, the concept of ‘levels of organization’ has received relatively little attention in its own right. I propose here an emerging approach that posits ‘levels’ as a fragmentary concept situated within an interest-relative matrix of operational usage within scientific practice. To this end I propose one important component of meaning, namely the epistemic goal motivating the term’s usage, which recovers a remarkably conserved and sufficiently unifying significance attributable to ‘levels’ across different instances of usage. This epistemic goal, to (...) provide structure to scientific problems, delegates tasks whose execution generates the term’s expressed content in a given instance. This treatment of levels does not diminish the concept’s general importance to science, but rather allows for its use in, and usefulness for, scientific practice to be better contextualized to particular tasks encompassing varying breadths of activity. (shrink)

The paper discusses how systems biology is working toward complex accounts that integrate explanation in terms of mechanisms and explanation by mathematical models—which some philosophers have viewed as rival models of explanation. Systems biology is an integrative approach, and it strongly relies on mathematical modeling. Philosophical accounts of mechanisms capture integrative in the sense of multilevel and multifield explanations, yet accounts of mechanistic explanation have failed to address how a mathematical model could contribute to such explanations. I discuss how mathematical (...) equations can be explanatorily relevant. Several cases from systems biology are discussed to illustrate the interplay between mechanistic research and mathematical modeling, and I point to questions about qualitative phenomena, where quantitative models are still indispensable to the explanation. Systems biology shows that a broader philosophical conception of mechanisms is needed, which takes into account functional-dynamical aspects, interaction in complex networks with feedback loops, system-wide functional properties such as distributed functionality and robustness, and a mechanism’s ability to respond to perturbations. I offer general conclusions for philosophical accounts of explanation. (shrink)

This essay analyzes and develops recent views about explanation in biology. Philosophers of biology have parted with the received deductive-nomological model of scientific explanation primarily by attempting to capture actual biological theorizing and practice. This includes an endorsement of different kinds of explanation (e.g., mathematical and causal-mechanistic), a joint study of discovery and explanation, and an abandonment of models of theory reduction in favor of accounts of explanatory reduction. Of particular current interest are philosophical accounts of complex explanations that appeal (...) to different levels of organismal organization and use contributions from different biological disciplines. The essay lays out one model that views explanatory integration across different disciplines as being structured by scientific problems. I emphasize the philosophical need to take the explanatory aims pursued by different groups of scientists into account, as explanatory aims determine whether different explanations are competing or complementary and govern the dynamics of scientific practice, including interdisciplinary research. I distinguish different kinds of pluralism that philosophers have endorsed in the context of explanation in biology, and draw several implications for science education, especially the need to teach science as an interdisciplinary and dynamic practice guided by scientific problems and explanatory aims. (shrink)

Evolutionary transitions in individuality (ETIs) are events during which individuals at a given level of organization (particles) interact to form higher-level entities (collectives) which are then recognized as new individuals at that level. ETIs are intimately related to levels of selection, which, following Okasha, can be approached from two different perspectives. One, referred to as ‘synchronic’, asks whether selection occurs at the collective level while the partitioning of particles into collectives is taken for granted. The other, referred to as ‘diachronic’, (...) asks about the origins of the partitioning of particles into collectives. After having presented the two perspectives and a classical formalism used to deal with the levels-of-selection question in the literature, namely the multilevel version of the Price equation, I show that because this formalism treats the levels-of-selection question from a synchronic perspective, it is inadequate to explain ETIs. This is because a fundamental aspect of ETIs is the origin of collectives. From there, I develop a framework for levels of selection compatible with the diachronic perspective. This framework relies on the distinction between what I call, on the one hand, a ‘functional aggregative collective trait’, and on the other hand, a ‘functional non-aggregative collective trait’. After having presented this distinction, I implement it in the Price equation, leading to a new statistical partitioning of this equation which, I argue, represents a causal decomposition more relevant for ETIs. Finally, I exploit this partitioning to explain the critical stages of an ETI. In addition to its explanatory power, a measure of the degree of functional non-aggregativity could be used as a proxy for the degree of individuality of a collective. (shrink)

The formalism used to describe evolutionary change in a multilevel setting can be used equally to re-describe the situation as one where all the selection occurs at the individual level. Thus, whether multilevel or individual-level selection occurs seems to be a matter of convention rather than fact. Yet, group selection is regarded by some as an important concept with factual rather than conventional elements. I flesh out an alternative position that regards groups as a target of selection in a way (...) that is not merely definitional fiat and provide a theoretical basis for this position. (shrink)

In the past decades, reductionism has dominated both research directions and funding policies in clinical psychology and psychiatry. The intense search for the biological basis of mental disorders, however, has not resulted in conclusive reductionist explanations of psychopathology. Recently, network models have been proposed as an alternative framework for the analysis of mental disorders, in which mental disorders arise from the causal interplay between symptoms. In this target article, we show that this conceptualization can help explain why reductionist approaches in (...) psychiatry and clinical psychology are on the wrong track. First, symptom networks preclude the identification of a common cause of symptomatology with a neurobiological condition; in symptom networks, there is no such common cause. Second, symptom network relations depend on the content of mental states and, as such, feature intentionality. Third, the strength of network relations is highly likely to depend partially on cultural and historical contexts as well as external mechanisms in the environment. Taken together, these properties suggest that, if mental disorders are indeed networks of causally related symptoms, reductionist accounts cannot achieve the level of success associated with reductionist disease models in modern medicine. As an alternative strategy, we propose to interpret network structures in terms of D. C. Dennett's (1987) notion ofreal patterns, and suggest that, instead of being reducible to a biological basis, mental disorders feature biological and psychological factors that are deeply intertwined in feedback loops. This suggests that neither psychological nor biological levels can claim causal or explanatory priority, and that a holistic research strategy is necessary for progress in the study of mental disorders. (shrink)

Mechanistic models in molecular systems biology are generally mathematical models of the action of networks of biochemical reactions, involving metabolism, signal transduction, and/or gene expression. They can be either simulated numerically or analyzed analytically. Systems biology integrates quantitative molecular data acquisition with mathematical models to design new experiments, discriminate between alternative mechanisms and explain the molecular basis of cellular properties. At the heart of this approach are mechanistic models of molecular networks. We focus on the articulation and development of mechanistic (...) models, identifying five constraints which guide the articulation of models in molecular systems biology. These constraints are not independent of one another, with the result that modeling becomes an iterative process. We illustrate the use of these constraints in the modeling of the mechanism for bistability in the lac operon. (shrink)