Poliseli LuanaCoutinho Jeferson G. E.Viana BlandinaRusso Federica...
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查看更多>>摘要：Abstract This article addresses the contributions of the literature on the new mechanistic philosophy of science for the scientific practice of model building in ecology. This is reflected in a one-to-one interdisciplinary collaboration between an ecologist and a philosopher of science during science-in-the-making. We argue that the identification, reconstruction and understanding of mechanisms is context-sensitive, and for this case study mechanistic modeling did not present a normative role but a heuristic one. We expect our study to provides useful epistemic tools for the improvement of empirically-riven work in the debates about mechanistic explanation of ecological phenomena.
查看更多>>摘要：Abstract We argue that cognitive functions are not reducible to biological functionality. Since only neural animals can develop complex forms of agency, we assume that genuinely cognitive processes are deeply related with the activity of the nervous system. We first analyze the significance of the appearance of the nervous system in certain multicellular organisms (i.e., eumetazoa), arguing that it has changed the logic of their biological organization. Then, we focus on the appearance of specifically cognitive capacities within the nervous system. Considering a case of a minimal form of perceptual representation (as it happens in the visual system of cubozoan medusae), we analyze the specific functional role of this minimal form of (cognitive) activity in relatively earlier nervous systems, arguing that though this role is only understandable within a biological organization, yet it is not reducible to the underlying biological functionality. Finally, we conclude that the appearance of cognition is in turn linked to the emergence of an autonomous neurodynamic domain and a qualitative change in body complexity.
查看更多>>摘要：Abstract There are many decision contexts in which we require accurate information on animal welfare, in ethics, management, and policy. Unfortunately, many of the methods currently used for estimating animal welfare in these contexts are subjective and unreliable, and thus unlikely to be accurate. In this paper, I look at how we might apply principled methods from animal welfare science to arrive at more accurate scores, which will then help us in making the best decisions for animals. I construct and apply a framework of desiderata for welfare measures, to assess the best of the currently available methods and argue that a combined use of both a whole-animal measure and a combination measurement framework for assessing welfare will give us the most accurate answers to guide our action.
查看更多>>摘要：Abstract We here develop a concept of an individualized niche in analogy to Hutchison’s population-level concept of the ecological niche. We consider the individualized (ecological) niche as the range of environmental conditions under which a particular individual has an expected lifetime reproductive success of ≥?1. Our concept has primarily an ecological function, as it refers to the match of an individual phenotype to its contemporary environment (niche fit) while we discuss evolutionary fitness as an evaluative parameter of this fit. We address four specific challenges that occur when scaling the niche down from populations to individuals. In particular, we discuss (1) the consequences of uniqueness of individuals in a population and the corresponding lack of statistical replication, (2) the dynamic nature of individualized niches and how they can be studied either as time-slice niches, as prospective niches or as trajectory-based niches, (3) the dimensionality of the individualized niche, that is greater than the population niche due to the additional dimensions of intra-specific niche space, (4) how the boundaries of individualized niche space can be defined by expected lifetime reproductive success and how expected reproductive success can be inferred by marginalizing fitness functions across phenotypes or environments. We frame our discussion in the context of recent interest in the causes and consequences of individual differences in animal behavior.
查看更多>>摘要：Abstract The notion of biological function is fraught with difficulties—intrinsically and irremediably so, we argue. The physiological practice of functional ascription originates from a time when organisms were thought to be designed and remained largely unchanged since. In a secularized worldview, this creates a paradox which accounts of functions as selected effect attempt to resolve. This attempt, we argue, misses its target in physiology and it brings problems of its own. Instead, we propose that a better solution to the conundrum of biological functions is to abandon the notion altogether, a prospect not only less daunting than it appears, but arguably the natural continuation of the naturalisation of biology.
查看更多>>摘要：Abstract It is often thought that non-junk or coding DNA is more significant than other cellular elements, including so-called junk DNA. This is for two main reasons: (1) because coding DNA is?often?targeted by historical or current selection, it is considered functionally special and (2) because its mode of action is uniquely specific amongst the other actual difference makers in the cell,?it is?considered causally special. Here, we challenge both these presumptions. With respect to function, we argue that there is previously unappreciated reason to think that junk DNA is significant, since it can alter the cellular environment, and those alterations can influence how organism-level selection operates. With respect to causality, we argue that there is again reason to think that junk DNA is significant, since it too (like coding DNA) is remarkably causally specific (in Waters’, in J Philos 104:551–579, 2007 sense). As a result, something is missing from the received view of significance in molecular biology—a view which emphasizes specificity and neglects something we term ‘reach’. With the special case of junk DNA in mind, we explore how to model and understand the causal specificity, reach, and corresponding efficacy of difference makers in biology. The account contains implications for how evolution shapes the genome, as well as advances our understanding of multi-level selection.
查看更多>>摘要：Abstract Reconstructing ancestral species is a challenging endeavour: fossils are often scarce or enigmatic, and inferring ancestral characters based on novel molecular approaches (e.g. comparative genomics or developmental genetics) has long been controversial. A key philosophical challenge pertinent at present is the lack of a theoretical framework capable of evaluating inferences of homology made through integration of multiple kinds of evidence (e.g. molecular, developmental, or morphological). Here, I present just such a framework. I start with a brief history and critical assessment of attempts at inferring morphological homology through developmental genetics. I then bring attention to a recent model of homology, namely Character Identity Mechanisms (DiFrisco et al. 2020), intended partly to elucidate the relationships between morphological characters, developmental genetics, and homology. I utilise and build on this model to construct the evaluative framework mentioned above, which judges the epistemic value of evidence of each kind in each particular case based on three proposed criteria: effectiveness, admissibility, and informativity, as well as providing a generalised guideline on how it can be scientifically operationalised. I then point out the evolution of the eumetazoan body plan as a case in point where the application of this framework can yield satisfactory results, both empirically and conceptually. I will conclude with a discussion on some potential implications for more general philosophy of biology and philosophy of science, especially surrounding evidential integration, models and explanation, and reductionism.
查看更多>>摘要：Abstract We examine the epistemological foundations of a leading technique in the search for evidence of life on exosolar planets. Specifically, we consider the “transit method” for spectroscopic analysis of exoplanet atmospheres, and the practice of treating anomalous chemical compositions of the atmospheres of exosolar planets as indicators of the potential presence of life. We propose a methodology for ranking the anomalousness of atmospheres that uses the mathematical apparatus of support vector machines, and which aims to be agnostic with respect to the particular chemical biosignatures of life. We argue that our approach is justified by an appeal to the “hinge” model of epistemic justification first proposed by as reported by Wittgenstein (On certainty, Blackwell, Oxford, 1969). We then compare our approach to previous work due to Walker et al. (Astrobiology 18(6):779–824, 2018) and Cleland (Astrobiology 19(6):722–729, 2019a; Does ‘life’ have a definition?, Cambridge University Press, New York, 2019b).
查看更多>>摘要：Abstract Over the last fifteen years, an ambitious explanatory framework has been proposed to unify explanations across biology and cognitive science. Active inference, whose most famous tenet is the free energy principle, has inspired excitement and confusion in equal measure. Here, we lay the ground for proper critical analysis of active inference, in three ways. First, we give simplified versions of its core mathematical models. Second, we outline the historical development of active inference and its relationship to other theoretical approaches. Third, we describe three different kinds of claim—labelled mathematical, empirical and general—routinely made by proponents of the framework, and suggest dialectical links between them. Overall, we aim to increase philosophical understanding of active inference so that it may be more readily evaluated. This paper is the Introduction to the Topical Collection “The Free Energy Principle: From Biology to Cognition”.
查看更多>>摘要：Abstract The distinction between causal role (CR) and selected effect (SE) functions is typically framed in terms of their respective explanatory roles. However, much of the controversy over functions in genomics takes place in an investigative, not an explanatory context. Specifically, the process of component-driven functional investigation begins with the designation of some genetic or epigenetic element as functional —i.e. not junk— because it possesses properties that, arguably, suggest some biologically interesting organismal effect. The investigative process then proceeds, in a bottom-up fashion, to search for those effects. I argue that this process encounters a problem reminiscent of one that Gould and Lewontin (1979) associated with the adaptationist program. Just as their stereotypical adaptationst became trapped in the myopic pursuit of one selectionist hypothesis after another, so can the investigation of CR functions in genomics lead to an unending series putative organism-level CR functions for junk DNA. This is an acute problem for genomics, because (1) eukaryotic genomes are littered with transposable elements (TEs) and their deactivated descendants which (2) often masquerade as interesting CR-functional components and (3) it is experimentally onerous to determine whether they lack such a function. I further argue that selectionist reasoning about TE-host coevolutionary dynamics can greatly streamline the investigative process. Importantly, selectionist hypotheses need not be well confirmed to be illuminating in this context. Informed selectionist reasoning about the strategic roles of TEs in the genome offers a corrective to the idea that most of our DNA is somehow CR (and possibly SE) functional for the organism.
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