Biology & Philosophy

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Article
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.
 
Article
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.
 
Article
The free energy principle is notoriously difficult to understand. In this paper, we relate the principle to a framework that philosophers of biology are familiar with: Ruth Millikan’s teleosemantics. We argue that: (i) systems that minimise free energy are systems with a proper function; and (ii) Karl Friston’s notion of implicit modelling can be understood in terms of Millikan’s notion of mapping relations. Our analysis reveals some surprising formal similarities between the two frameworks, and suggests interesting lines of future research. We hope this will aid further philosophical evaluation of the free energy principle.
 
Article
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”.
 
Article
Organisms live not as discrete entities on which an independent environment acts, but as members of a reproductive lineage in an ongoing series of interactions between that lineage and a dynamic ecological niche. These interactions continuously shape both systems in a reciprocal manner, resulting in the emergence of reliably co-occurring configurations within and between both systems. The enactive approach to cognition describes this relationship as the structural coupling between an organism and its environment; similarly, Developmental Systems Theory emphasizes the reciprocal nature of structurally coupled systems in its analysis of organisms as developmental processes embedded within a developmental system. Through an enactive-developmental systems framing, this paper identifies the organizational features of cognizing systems in order to motivate a picture of how organism and environment co-determine and co-construct one another. I argue that organisms can be characterized as self-organizing, operationally closed, plastic systems ecologically embedded within a developmental system. In virtue of this organizational makeup, organisms actively engage in the modulation and assessment of their coupling with their environment: cognitive strategies that entail contextualized responses to variations across the web of interactions that comprises the developmental system.
 
Article
The validity and utility of the proximate-ultimate distinction in biology have recently been under debate. Opponents of the distinction argue that it rules out individual-level organismic processes from evolutionary explanations, thereby leading to an unfounded separation between organismic (developmental, behavioral, etc.) causation and evolutionary causation. Proponents of the proximate-ultimate distinction, on the other hand, argue that it serves an important epistemological role in forming different kinds of explanation-seeking questions in biology. In this paper we offer an interpretation the proximate-ultimate distinction not only as a means of forming explanation-seeking questions, but also as a distinction that can help highlight the way in which individual-level organismic processes can be evolutionary causes. We do this by interpreting the distinction between proximate and ultimate causes as a distinction between structuring and triggering causes.
 
Various causes with distinct combinations of specificity, reach, and corresponding efficacy. Top left, an utterly inefficacious cause with no effects. Bottom right, an extremely efficacious cause—one that has both reach and specificity in terms of its effects. Reach is indicated by number of nodes—where each cause can have either unitary or multiple effects, both proximate and ultimate. Causal specificity is indicated by effect opacity—where each node can either transmit its full pigmentation or produced a faded node with increased transparency. Within rows, causes increase in specificity from left to right; within columns, causes increase in reach from top to bottom. Hence, top right has more specificity though less reach relative to bottom left, which has more reach though less specificity. Both are less efficacious than bottom right, but more efficacious than top left; neither are necessarily insignificant causes. (Prepared by Adam Streed using the matplotlib library for Python 3; all the code is his own)
Various genetic causes with distinct combinations of specificity, reach, and corresponding efficacy. a A synonymous, conservative mutation in any transcribed DNA—coding or junk. b A synonymous, semi-conservative mutation in coding DNA. c A non-synonymous, semi-conservative mutation in coding DNA—one that produces a change in protein amino acid sequence but no change in conformation. d A non-synonymous, non-conservative mutation in coding DNA—a genotypic change with phenotypic and other ultimate effects. e Insertion or deletion of a small “repeat” segment of junk DNA. f Insertion or deletion of a large “repeat” segment of junk DNA—one which ultimately produces an uptick in RNA decay machinery. g Insertion or deletion of a large, unique (not a repeat) segment of junk DNA—the size rather than uniqueness of which also produces an uptick in RNA decay machinery. h Insertion or deletion of another large, unique segment of junk DNA—one that produces in virtue of its size and uniqueness not just an uptick in RNA decay machinery but also other downstream, causally non-specific distal effects. Explication of these cases continues in the main text below (Prepared by Adam Streed using the matplotlib library for Python 3; all the code is his own)
Article
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.
 
Article
Justin Garson has recently advanced a Generalised Selected Effects Theory of biological proper function. According to Garson, his theory spells trouble for the Dysfunction Account of Disorder. This paper argues that Garson’s critique of the Dysfunction Account from the Generalised Theory fails, and that we should reject the Generalised Theory outright. I first show that the Generalised Theory does not, as Garson asserts, imply that neurally selected disorders are not dysfunctional. Rather, it implies that they are both functional and dysfunctional. I argue on this basis that the Generalised Theory yields conflicting functional norms, and we that should reject it outright on these grounds.
 
Article
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.
 
How TEs could be both selfish and drivers of evolution. (1) Acquisition of transposable element (TE, indicated by shaded rectangle) by LGT to the recipient species from another species. (2) Generation of TE family by transposition of copies of the element, here to six of the seven chromosomes of an individual recipient. Each deposited copy inserted is at best neutral and unlikely to be fixed, and if fixed, only by drift. Nevertheless, if transposition is sufficiently frequent and occurs over a long enough time, any single individual may have numerous copies at many positions, many shared with others of the species, as depicted here. (3) A chance mutation to a transcription factor binding site (TFBS, indicated by a circle) for a factor active in the species increases transposition rate of mutant TEs, so TFBS-bearing TEs increase in frequency within the family. By chance, one copy of the TFBS-bearing TE inserts in one individual in such a way as to activate a gene (black box), the activation of which by the transcription factor is selected for within a species. So (4) this TE-enhanced allele on this chromosome will likely be fixed in the recipient species. Given the fact that most newly deposited TE copies are at best neutral and that members of this TE family are in constant competition with new variants in this and other families, copies (or remnants of copies) functioning as “drivers” of selected-for genes may in time be the only detectable members of the original TE family left. Thus in the initial (“selfish”) stage of family establishment, selection is at the level of the element. In the later (“driver”) stage it is at the level of the organism
A summary of the scheme of TE family evolution presented in Fig. 1. Solid line indicates TE family members detectable by sequence. Dashed line indicates the fraction of total detectable members that perform fitness-enhancing “functions” at the organism level
Article
The origin and prevalence of transposable elements (TEs) may best be understood as resulting from “selfish” evolutionary processes at the within-genome level, with relevant populations being all members of the same TE family or all potentially mobile DNAs in a species. But the maintenance of families of TEs as evolutionary drivers, if taken as a consequence of selection, might be better understood as a consequence of selection at the level of species or higher, with the relevant populations being species or ecosystems varying in their possession of TEs. In 2015, Brunet and Doolittle (Genome Biol Evol 7: 2445–2457) made the case for legitimizing (though not proving) claims for an evolutionary role for TEs by recasting such claims as being about species selection. Here I further develop this “how possibly” argument. I note that with a forgivingly broad construal of evolution by natural selection (ENS) we might come to appreciate many aspects of Life on earth as its products, and TEs as—possibly—contributors to the success of Life by selection at several levels of a biological hierarchy. Thinking broadly makes this proposition a testable (albeit extraordinarily difficult-to-test) Darwinian one.
 
Character Identity Mechanisms are evolutionarily stable relative to upstream signals (positional information) and downstream effectors (realiser genes), as represented by the hourglass figure; modified from (DiFrisco et al. 2020)
Effectiveness, admissibility, and informativity of developmental evidence when integrated with morphological evidence. The x axis represents confidence in developmental genetic homology, the y axis represents confidence in morphological homology based on morphological evidence alone, and the z axis represents degree of association (= correlation) between the two traits across a clade. All three parameters range (-1, 1)
An algorithmic model of integrating developmental and morphological evidence, corresponding to the first, correlational level of integration and the application of the three criteria. The last step in the process forms the basis of the second, causal/mechanistic level of integration: as homology is suggested by the correlational analysis, it can be further confirmed or refuted by experimental evidence, which can then feed into further correlational analysis
Interaction between Wnt and BMP signalling gradients in the early embryo of a cnidarian, giving rise to a bilateral body plan in later stages, representing (as a proxy) the ancestral eumetazoan; modified from (Genikhovich and Technau 2017)
Article
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.
 
Article
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.
 
Article
Constructive Neutral Evolution (CNE) theory provides selectively neutral explanations of the origin and maintenance of biological complexity. This essay provides an analysis of CNE as an explanatory strategy defined by a tripartite set of conditions, and shows how this applies to cases of the evolution of complexity at higher-levels of the biological hierarchy. CNE was initially deployed to help explain a variety of complex molecular structures and processes, including spliceosomal splicing, trypansomal pan-editing, scrambled genes in ciliates, duplicate gene retention and fungal ATP synthetase structure. CNE has also been generalized to apply to phenomena at the cellular level, including protein-protein interaction network modulatory, obligate microbial symbioses, eukaryogenesis and microbial unculturability. This essay further extends the CNE to cases of complexity at levels of organization higher than the molecular and cellular. These are (1) multicellular phenotypic complexity, (2) multicellular ecological complexity and, (3) some cases of cultural complexity.
 
Article
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 provide useful epistemic tools for the improvement of empirically-driven work in the debates about mechanistic explanations of ecological phenomena.
 
Diagram illustrating the trade-offs associated with different approaches to inquiry in astrobiology. An approach is represented as a point in the triangle, with points near the far left corner being closest to an approach based entirely on Bayesian inference, approaches in the far right corner being closest to an approach based entirely on unsupervised anomaly-detection algorithms, and points near the top-middle corner being closest to an approach based entirely on a specific theory of life. The strengths and weaknesses of each of these varieties of approach are listed in the diagram, and points inherit these strengths and weaknesses to the extent that they are situated in proximity to the corner in question. Our approach is closest to the algorithmic extreme, but does incorporate some biological theory due to its reliance on metabolism, and also incorporates the transparency of Bayeisan approaches. By contrast, we view Walker et al.’s approach as an amalgamation of the Bayesian formalism, but with a prior that reflects a commitment to a particular theory
Article
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 Wittgenstein (1969). We then compare our approach to previous work due to Walker et al. (2018) and Cleland (2019a, 2019b).
 
Relationships between Wouters' (2003) four notions of function
Article
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.
 
Article
Philosophers who study the problem of biological function often begin their deliberations by reflecting on the functions of parts of animals, or the behavior of animals. Applying theories of biological function to unconventional or borderline cases can help us to better evaluate and refine those theories. This is the case when we consider whether parts of transposable elements (TEs)—bits of “selfish” DNA that move about within a host genome—have functions of their own, that is, whether the parts of TEs have the function of helping the TE move about within the genome. Here I argue that whether or not the parts of TEs have functions depends crucially on whether collections of TEs form “populations,” by which I mean, here, a group of individuals of the same type that impact one another’s chances of persistence or multiplication, by impacting one another’s access to a shared resource. I think there is suggestive, but not conclusive, evidence that some TEs have functions of their own. Considering the problem of TE functionality, then, has value both for philosophy and for biology.
 
Article
The proper function of the heart is pumping the blood. According to what we call the type etiological view, this is because previous tokens of the type HEART were selected for pumping the blood. Nanay (J Philos 107(8):412–431, 2010) argues that the type etiological view is viciously circular. He claims that the only plausible accounts of trait type individuation use proper functions, such that whenever the type etiological view is supplemented with a plausible account of trait type individuation, the result is a view that uses proper functions to explain proper functions. We refine this objection, and argue that Nanay at most establishes a potentially benign definitional circularity. However, we show that the type etiological view’s reliance on types nevertheless generates a vicious regress. Hence the type etiological view is false. We reject dispositional and modal alternatives to the type etiological view for the reason that they either cannot accommodate malfunction, or do so at the cost of proliferation; and then formulate a novel token etiological view that overcomes both problems because it makes no reference to trait types.
 
Article
Are there nonhuman animals who behave morally ? In this paper I answer this question in the affirmative by applying the framework of care ethics to the animal morality debate. According to care ethics, empathic care is the wellspring of morality in humans. While there have been several suggestive analyses of nonhuman animals as empathic, much of the literature within the animal morality debate has marginalized analyses from the perspective of care ethics. In this paper I examine care ethics to extract its core commitments to what is required for moral care: emotional motivation that enables the intentional meeting of another’s needs, and forward-looking responsibility in particular relationships. What is not required, I argue, are metarepresentational capacities or the ability to scrutinize one’s reasons for action, and thus being retrospectively accountable. This minimal account of moral care is illustrated by moral practices of parental care seen in many nonhuman animal species. In response to the worry that parental care in nonhuman animals lacks all evaluation and is therefore nonmoral I point to cultural differences in human parenting and to normativity in nonhuman animals.
 
A series of particular events as an instantiation of an abstract event structure. The boxes at the top represent connected type events that typically lead to a type phenomenon. The boxes at the bottom represent connected particular events in the evolution and dissemination of ST8 that have led to a particular state of the ST8 clade (see Strauß et al. 2017, E10601).
Article
Historical explanations in evolutionary biology are commonly characterized as narrative explanations. Examples include explanations of the evolution of particular traits and explanations of macroevolutionary transitions. In this paper, I present two case studies of explanations in accounts of pathogen evolution and host-pathogen coevolution, respectively, and argue that one of them is captured well by established accounts of time-sequenced narrative explanation. The other one differs from narrative explanations in important respects, even though it shares some characteristics with them as it is also a population-level historical explanation. I thus argue that the second case represents a different kind of explanation that I call historical explanation of type phenomena. The main difference between the two kinds of explanation is the conceptualization of the explanandum phenomena as a particulars or type phenomena, respectively. Narrative explanations explain particulars but also deal with generalization, regularities and type phenomena. Historical explanations of type phenomena, on the other hand, explain multiply realizable phenomena but also deal with particulars. The two kinds of explanation complement each other because they explain different aspects of evolution.
 
The relationship between the realized and fundamental niches according to (a) Hutchinson (1957), (b) Bruno et al. (2003), and (c) Rodriguez-Cabal et al. (2012). In (a), negative interactions (competition, predation, parasitism) make the realized niche (grey circle) smaller than the fundamental niche (black line). In (b), facilitation makes the realized niche (grey circle) larger than the fundamental niche (black line). In (c), facilitation mitigates the effects of negative interactions and makes the realized niche (grey circle) larger than it would be without facilitation (its size in a), but does not make it larger than the fundamental niche (black line).
Adapted from Rodriguez-Cabal et al. (2012, p. 37)
A geographical application of the realized/fundamental niche contrast. The species’ niche without facilitation (left) covers less geographical space than its niche with facilitation (right). If the niche without facilitation (right) is assumed to represent what the species’ (geographical) niche would be if no interaction with other species occurred, then this niche can be called its (geographical) fundamental niche, and its geographical niche as expanded by facilitation (right) can be called its realized (geographical) niche
The realized environmental space with respect to two ecological factors, and a species’ fundamental, potential, and realized niches with respect to these two factors. The realized environmental space comprises the combinations of values of the two factors that are instantiated in a location. The species’ fundamental niche comprises the combinations of values of the two environmental factors that would permit the species to persist indefinitely if not hindered by another species. The potential niche comprises the intersection of the realized environmental space and the fundamental niche. The realized niche comprises the portion of the potential niche in which the specie’s presence it not hindered by the presence of another species whose fundamental niche partly overlaps with its own.
Adapted from Jackson and Overpeck (2000, p. 197)
A species’ realized niche without and with the presence of a competitor. The subset of the potential niche occupied by the species changes, but the size of the potential niche remains unchanged (the size of the fundamental niche also remains unchanged). Inspired by Jackson and Overpeck (2000, p. 197)
A species’ realized niche without and with the presence of a facilitator. The size of the potential niche changes and this affects the size of the realized niche (the size of the fundamental niche also remains unchanged). Inspired by Jackson and Overpeck (2000, p. 197)
Article
This paper revisits the debate over whether the study of facilitation requires ecologists to revise their understanding of the relationship between realized and fundamental niches as conceptualized by Hutchinson. Following Rodriguez-Cabal et al. (2012), I argue against Bruno et al.’s (2003) claim that facilitation can make a species’ realized niche larger than its fundamental niche. However, I also maintain that the abstract Hutchinsonian conceptualization of the niche makes a whole range of facilitative interactions—which I propose to call ameliorative facilitation—invisible to niche-based approaches to the study of ecological communities. I propose a way to incorporate ameliorative facilitation into such approaches. My proposal involves supplementing the Hutchinsonian realized/fundamental dyad with a third concept: the potential niche. This concept was introduced by ecologists studying the effects of environmental change on species distributions (Jackson and Overpeck 2000), but I show how it could also be fruitfully used in facilitation studies. I argue that this proposed solution is more appealing than Stachowicz’s (2012) suggestion that Hutchinson’s realized/fundamental contrast be applied to a spatial-geographical, as opposed to an abstract-conceptual, notion of the niche.
 
Article
Can we read emotions in faces? Many studies suggest that we can, yet skeptics contend that these studies employ methods that unwittingly help subjects in matching faces with emotions. Some studies present subjects with posed faces, which may be more exaggerated than spontaneous ones. And some studies provide subjects with a list of emotion words to choose from, which forces them to interpret faces in specific emotion terms. I argue that the skeptics’ challenge rests on a false assumption: that once subjects leave the lab, they no longer receive help in matching faces with emotions. I contend that people receive as much help in the wild as they do in the lab. People unconsciously amplify their spontaneous expressions in the presence of others, thereby making them easier to read. And people teach children to interpret faces in the same specific emotion terms found in the experimenters’ word lists. I argue that we are good at readings emotions in faces because we can normally count on a little help from our friends.
 
The ratio of protein to carbohydrate intake and its effects on growth and survival in locusts (reproduced from (Raubenheimer and Simpson 2020))
Two examples demonstrating regulation towards an intake target. In (a), the dark circles depict the results of locusts altering the amounts of given food pairings (represented by the lines or ‘rails’ indicating distinct nutrient ratios of proteins to carbohydrates) and converging on a target. The open squares show what would be expected if the locusts were not balancing. In (b), cockroaches were initially confined to one of three imbalanced foods (represented by the dotted lines/rails) and then given free choice of all three. The shapes represent groups of cockroaches starting from these distinct imbalanced foods, and the subsequent series shows their cumulative intake over time. By combining these foods, each group of cockroaches redressed their respective imposed imbalances and converged on the same target ratio (reproduced with permission from (Raubenheimer et al. 2012))
Article
While philosophers of science have marginally discussed concepts such as ‘nutrient’, ‘naturalness’, ‘food’, or the ‘molecularization’ of nutrition, they have yet to seriously engage with the nutrition sciences. In this paper, I offer one way to begin this engagement by investigating conceptual challenges facing the burgeoning field of nutritional ecology and the question of how organisms construct a ‘balanced’ diet. To provide clarity, I propose the distinction between nutrient balance as a property of foods or dietary patterns and nutrient balancing as an evolved capacity to regulate nutrient intake. This distinction raises conceptual and empirical issues, such as what properties constitute this capacity and whether they are the same in all organisms. Additionally, while scientists use the term ‘balancing’, its intension and extension need further clarification. Based on the literature, the properties of external nutrient detection, internal sensing of nutrient levels, and organismal regulation could provide a basic recipe for nutrient balancing. Next, using an evolutionary lens, I examine nutrient acquisition in some prokaryotes, slime molds, simple multicellular eukaryotes, and in the quirks of multicellular metabolism to raise questions about the origins and universality of balancing. Finally, I build on this explication of balance and balancing by considering how obesity and cancer might respectively elucidate problems of organismal nutrient imbalances versus disrupted cellular nutrient balancing. http://philsci-archive.pitt.edu/20344/
 
The form of the niche. For each resource r, U is the probability of its utilization in a unit time by an individual. The area under each curve, therefore, is the total resource utilization Ki for species i
Article
The niche is allegedly the conceptual bedrock underpinning the most prominent, and some would say most important, theorizing in ecology. We argue this point of view is more aspirational than veridical. Rather than critically dissect existing definitions of the concept, the supposedly significant work it is thought to have done in ecology is our evaluative target. There is no denying the impressive mathematical sophistication and theoretical ingenuity of the ecological modeling that invokes ‘niche’ terminology. But despite the pervasive labeling, we demonstrate that niche talk is nothing more than a gloss on theory developed without it, that doesn’t need it, and that doesn’t benefit from it.
 
Article
Humans are standouts in their propensity to trade. More specially, the kind of trading found in humans—featuring the exchange of many different goods and services with many different others, for the mutual benefit of all the involved parties—far exceeds anything that is found in any other creature. However, a number of important questions about this propensity remain open. First, it is not clear exactly what makes this propensity so different in the human case from that of other animals. Second, it is not clear why other animals did not acquire this propensity to the extent that humans did. Third, it is not clear what explains the fact that the extent to which humans engage in trade is culturally highly variable. The paper argues that at the heart of the human-animal divergence in this propensity is the particular socio-cultural environment in which humans evolved. This has led them to sometimes, but not always, acquire the cognitive technology (writing, algebra, tallying devices, money, etc.) to support a sophisticated disposition and capacity for reciprocal cooperation, and deep and wide concepts of property and exchange value.
 
Article
Showing that the arithmetic mean number of offspring for a trait type often fails to be a predictive measure of fitness was a welcome correction to the philosophical literature on fitness. While the higher mathematical moments (variance, skew, kurtosis, etc.) of a probability-weighted offspring distribution can influence fitness measurement in distinct ways, the geometric mean number of offspring is commonly singled out as the most appropriate measure. For it is well-suited to a compounding (multiplicative) process and is sensitive to variance in offspring number. The geometric mean thus proves to be a predictively efficacious measure of fitness in examples featuring discrete generations and within- or between-generation variance in offspring output. Unfortunately, this advance has subsequently led some to conclude that the arithmetic mean is never (or at best infrequently) a good measure of fitness and that the geometric mean should accordingly be the default measure of fitness. We show not only that the arithmetic mean is a perfectly reasonable measure of fitness so long as one is clear about what it refers to (in particular, when it refers to growth rate), but also that it functions as a more general measure when properly interpreted. It must suffice as a measure of fitness in any case where the geometric mean has been effectively deployed as a measure. We conclude with a discussion about why the mathematical equivalence we highlight cannot be dismissed as merely of mathematical interest.
 
Article
The very idea of novel ecosystems has been controversial in ecology. Critics have complained about its imprecision, and that it illicitly smuggles problematic ethical and political values into the science. By labelling a human-modified system a ‘novel ecosystem,‘ they worry, we give policymakers a “license to trash nature.“ The critics are right to be suspicious. I show that proponents of the novel ecosystem concept have been unable to make it both value-free and precise enough to allow for applied use. Also, the critics are right to be suspicious, because a goal for many proponents of novel ecosystems is to bring new values into applied ecology. But the critics are wrong that this is illicit. I defend a value-laden conception of novel ecosystems, showing that applied ecologists are comfortable with other value-laden concepts (e.g. invasive species), and that the value shift motivating discussion of novel ecosystems is necessary if we want to understand and protect nature in a changing world.
 
The rise of ‘biodiversity’ in English-language books
The rise of ‘biodiversity’ in the scientific literature
Article
This paper explores interactions between ecological science and conservation values in the biodiversity-ecosystem function (BEF) debate of the 1990–2000s. The scientific debate concerned the interpretation of observed correlations between species richness and ecosystem properties like primary productivity in experimental ecosystems. The debate over the causal or explanatory role of species richness was presumed to have implications for conservation policy, and the use of such research to support policy recommendations generated hostility between rival groups of ecologists. I argue that the debate was due in part to the adoption of a broad conception of biodiversity as a goal and value in conservation politics and ethical debates, and the ecologists who questioned the causal efficacy of species richness were also suggesting problems with this goal. I characterize what I call the “uneasy consensus” established by BEF researchers in the late 2000s, discuss roles for values in BEF research, and suggest that this episode shows that ecological science can itself be an important site for ethical debates about conservation values.
 
Assumptions underlying common conceptions of the enemy release hypothesis, depicted as a causal network diagram for the case of plant invasions. a The general version of the hypothesis is similar to a black box, i.e. detailed causes are not given explicitly. b, c Causal network diagrams could be used to describe the hypothesized underlying mechanism in greater detail. Light blue nodes show added information. Arrows depict hypothesized causal relationships
Original formulation of the enemy release hypothesis, translated into a causal network diagram. a In its original version suggested by Keane and Crawley (2002), the enemy release hypothesis consisted of a set of assumptions about plant species in their native range and processes occurring during the course of the invasion. b Besides this general formulation of the hypothesis, additional assumptions about the mechanism were given in the main text (added here in light blue). Arrows depict hypothesized causal relationships
Article
Invasion ecology addresses the spread of species outside of their native ranges. A central aim of this field is to find mechanistic explanations for why species are able to establish and spread in an area in which they did not evolve. Usually it remains unclear, however, what exactly is meant by ‘mechanistic explanation’ or ‘mechanism’. The paper argues that the field can benefit from the philosophical discussion of what a mechanism is. Based on conceptions of mechanisms as processes in concrete systems, causal mechanisms can be defined as one type of mechanism, representing recurring networks of causal relationships. With the example of a well-known hypothesized mechanism in invasion ecology, namely enemy release, the paper demonstrates how such causal mechanisms can be depicted as causal network diagrams. This approach could facilitate the development of step-by-step explanations, enhance clear argumentation and allow for more precise linkage of empirical tests to theory. Challenges to assessing the empirical relevance of hypothesized mechanisms are discussed, and suggestions are made concerning how the proposed approach could help in overcoming some of them.
 
Article
Darwin’s claim about natural selection is reconstructed as an empirical claim about the causal relevance of the match between the individual and its environment for the condition of the individual, and the consequence of this condition for leaving progeny. It is shown that many fitness proxies are mediating between these two steps. They are indicators of the match and predictors of reproductive success at once. Modern concepts of fitness, in contrast, are focusing exclusively on the latter. Assuming that Darwin wanted to explain selection in terms of a modern concept of fitness thus confounds his argument. Taking the janiform character of fitness proxies serious, in contrast, does not only allow for integrating Darwin’s argument into current evolutionary biology, but also helps reframing and alleviating the dispute between the Modern Synthesis and the Extended Evolutionary Synthesis.
 
Article
Memories and emotions are both vital parts of everyday life, yet crucial interactions between the two have scarcely been explored. While there has been considerable research into how emotions can influence how well things are remembered, whether or not emotions themselves can be remembered is still a largely uncharted area of research. Philosophers and scientists alike have diverging views on this question, which seems to stem, at least in part, from different accounts of the nature of emotions. Here, I try to answer this question in a way that takes an intuitive notion of emotion and includes both scientific as well as philosophical aspects of both emotions and memory. To do this, I first distinguish between two different ways emotions can be expressed: as certain physiological responses, or as certain conscious experiences. Next, I show how each of these expressions of emotions can be remembered. Finally, I bring these two ways of expressing emotions, and the ways of remembering each of them, together into an explanation that also includes aspects often ascribed to emotions such as cognition. This interdisciplinary endeavor aims to serve as a starting point on what it could mean to remember emotions, and in doing so tries to build a bridge between scientific research and philosophical investigation of the memory of emotions.
 
Article
The overall objective of the study was to examine the pros and cons of the participatory approach adopted in natural resource management in the ecologically protected areas of the Sundarbans mangrove of Bangladesh. A comparative study was done between the people who are involved and non-involved in this approach. Empirical data was collected through personal interviews with a structured questionnaire. The Gini coefficient was measured first and then embedded with the Lorenz curve to draw a line between perfect equality and inequality vis-a-vis. The study revealed that the co-management built awareness in favor of biodiversity conservation and the efficient use of natural resources. Contradictorily, a segment of different hierarchical committees was involved in destructive activities like poisoning the wetlands for fishing. Therefore, a mixed outcome was found. The findings will help the policymakers in identifying the pitfalls and bottlenecks rooted in co-management. Hence, the study recommends revising the approach to ensure the community’s active participation on an equal basis and take action against them who degrade those resources. Exploring profitable alternative income-generating activities is warranted to narrow down the dependency on the Sundarbans mangrove’s natural resources. In order to address the tragedy of the commons, the study advocates for the unity of all knowledge ranging from science to humanistic scholarship for sound policymaking.
 
Article
Philosophy and anaesthesiology are disciplines that are rarely associated despite their respective interests in human consciousness. In this paper, we consider the advantages of integrating anaesthesiology and philosophy in the endeavour of discovering the neural correlates of state consciousness. We venture the following twopart argument. First, we argue that philosophical debates about the correlation conditions for state consciousness can be improved by focusing on how anaesthesiologists actually measure and study consciousness in practice. We present Integrated Information Theory as a promising framework for discriminating features hitherto considered relevant to the identification of the neural correlates of state consciousness. Second, we argue that an improved philosophical understanding of what comprises the correlation conditions for state consciousness can, in turn, advance anaesthesiological methodologies; not only can it improve how potential evidence is gathered and assessed, but it can aid in the prevention of intraoperative awareness, increasing patient safety and well-being.
 
Article
Cultural selection models aim to explain cultural phenomena as the products of a selective process, often characterising institutions, practices, norms or behaviours as adaptations. I argue that a lack of attention has been paid to the explanatory power of cultural selection frameworks. Arguments for cultural selection frequently depend on demonstrating only that selection models can in principle be applied to culture, rather than explicitly demonstrating the explanatory payoffs that could arise from their application. Understanding when and how cultural selection generates powerful explanations is crucial to evaluating cultural selection, as well as realising its promised epistemic and practical benefits. I argue that the ability for cultural selection to explain ‘design without a designer’ is crucial to successful and powerful cultural selection explanations. I introduce the strategy of comparing cultural selection to goal-directed agent accounts in order to evaluate when cultural selection can provide distinctive explanatory payoffs, drawing on two case studies to illustrate the benefits of this strategy. I argue that a focus on phenomena which cannot be explained through intention or agency-based explanations in particular could provide a fruitful avenue to identifying the cases where cultural selection can be insightfully applied.
 
Geometric patterns on Pseudodon DUB1006-fL, Trinil, Java, approx. 500 kya (Joordens et al. 2015, 230). Scales: 1cm (a, c), 1mm (d), none (b). Reprinted by permission from Nature Publishing Group
Geometric patterns on Artefact 1, Bilzingsleben, Germany, approx. 350 kya (Mania and Mania 1988, 93). Reprinted by permission from Rock Art Research
Article
Paleontological evidence suggests that human artefacts with intentional markings might have originated already in the Lower Paleolithic, up to 500.000 years ago and well before the advent of ‘behavioural modernity’. These markings apparently did not serve instrumental, tool-like functions, nor do they appear to be forms of figurative art. Instead, they display abstract geometric patterns that potentially testify to an emerging ability of symbol use. In a variation on Ian Hacking’s speculative account of the possible role of “likeness-making” in the evolution of human cognition and language, this essay explores the central role that the embodied processes of making and the collective practices of using such artefacts might have played in early human cognitive evolution. Two paradigmatic findings of Lower Paleolithic artefacts are discussed as tentative evidence of likenesses acting as material scaffolds in the emergence of symbolic reference-making. They might provide the link between basic abilities of mimesis and imitation and the development of modern language and thought.
 
The basic model of inference. An agent can observe x and must infer the value of w. The agent knows the statistical connection between them, encapsulated by the joint probability distribution p(w, x).
The basic model of action. An agent can produce an act, z, in order to bring about states w that in turn produce outcomes x. Active inference employs a controversial dual interpretation of p(w) and p(x) as probability distributions and preference distributions over hidden states and sensory states respectively.
Article
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 is a manuscript draft of the Introduction to the Topical Collection "The Free Energy Principle: From Biology to Cognition", forthcoming in Biology & Philosophy.
 
Article
The new mechanists and the autonomy approach both aim to account for how biological phenomena are explained. One identifies appeals to how components of a mechanism are organized so that their activities produce a phenomenon. The other directs attention towards the whole organism and focuses on how it achieves self-maintenance. This paper discusses challenges each confronts and how each could benefit from collaboration with the other: the new mechanistic framework can gain by taking into account what happens outside individual mechanisms, while the autonomy approach can ground itself in biological research into how the actual components constituting an autonomous system interact and contribute in different ways to realize and maintain the system. To press the case that these two traditions should be constructively integrated we describe how three recent developments in the autonomy tradition together provide a bridge between the two traditions: (1) a framework of work and constraints, (2) a conception of function grounded in the organization of an autonomous system, and (3) a focus on control.
 
Article
Epidemiological models directly shape policy responses to public health crises. We argue that they also play a less obvious but important role in solving certain coordination problems and social dilemmas that arise during pandemics. This role is both ethically and epistemically valuable. However, it also gives rise to an underappreciated dilemma, as the features that make models good at solving coordination problems are often at odds with the features that make for a good scientific model. We examine and develop this dilemma in the context of the COVID-19 pandemic, and suggest extensions to other domains.
 
Future-oriented weak intentional dynamics. The correlational rule (environmental state A will be followed by environmental state B) is internalized by an organism such that when A is sensed, future-oriented dynamics (red oval) are elicited and directed at B as a function of the organism’s homeostasis. Anticipatory behaviour, ß, despite its metabolic cost (or other short-term homeostasis destabilizing effects), is initiated prior to the coming about of B to ensure long-term homeostasis
A continuum of intentionality: above are some of the various research programmes which might be seen to investigate forms of cognitive phenomena associated with a particular degree of intentionality; below are some of the primary attributes of representational content as they are located at various places upon the continuum and capacities associated with them. When going from the weak end to the strong end of the continuum there is an increase in future-oriented-ness or how far into the future representational content can be directed
Article
Biogenic approaches investigate cognition from the standpoint of evolutionary function, asking what cognition does for a living system and then looking for common principles and exhibitions of cognitive strategies in a vast array of living systems – non-neural to neural. One worry which arises for the biogenic approach is that it is overly permissive in terms of what it construes as cognition. In this paper I critically engage with a recent instance of this way of criticising biogenic approaches in order to clarify their theoretical commitments and prospects. In his critique of the biogenic approach, Fred Adams (2018) uses the presence of intentional states with conceptual content as a criterion to demarcate cognition-driven behaviour from mere sensory response. In this paper I agree with Adams that intentionality is the mark of the cognitive, but simultaneously reject his overly restrictive conception of intentionality. I argue that understanding intentionality simpliciter as the mark of the mental is compatible with endorsing the biogenic approach. I argue that because cognitive science is not exclusively interested in behaviour driven by intentional states with the kind of content Adams demands, the biogenic approach’s status as an approach to cognition is not called into question. I then go on to propose a novel view of intentionality whereby it is seen to exist along a continuum which increases in the degree of representational complexity: how far into the future representational content can be directed and drive anticipatory behaviour. Understanding intentionality as existing along a continuum allows biogenic approaches and anthropogenic approaches to investigate the same overarching capacity of cognition as expressed in its different forms positioned along the continuum of intentionality. Even if all organisms engage in some behaviour that is driven by weak intentional dynamics, this does not suggest that every behaviour of all organisms is so driven. As such, the worry that the biogenic approach is overly permissive can be avoided.
 
Article
Recent discussions of animal communication and the evolution of language have advocated adopting a ‘pragmatics-first’ approach, according to which “a more productive framework” for primate communication research should be “pragmatics, the field of linguistics that examines the role of context in shaping the meaning of linguistic utterances” (Wheeler and Fischer, Evol Anthropol 21:195–205, 2012: 203). After distinguishing two different conceptions of pragmatics that advocates of the pragmatics-first approach have implicitly relied on (one Carnapian, the other Gricean), I argue that neither conception adequately serves the purposes of pragmatics-first approaches to the origins of human linguistic communication. My main aim in this paper is to motivate–and begin to articulate–an intermediary conception whose scope is narrower than Carnapian pragmatics but broader than Gricean pragmatics. To do so, I first spell out what I take to be the key insight offered by proponents of the Gricean approach concerning the emergence of linguistic communication, namely, its being communication ‘from a psychological point of view’ (Tomasello, Origins of human communication, MIT Press, Cambridge MA, 2008). I then develop this insight using key elements from the anti-Gricean ‘biosemantic’ account of linguistic communication due to Ruth Millikan (Millikan, Language, thought, and other biological categories: New foundations for realism, MIT Press, Cambridge MA, 1984, Millikan, Tomberlin (ed), Philosophical Perspectives 9, Ridgeview Publishing, Atascedero CA, 1995, Millikan R (2006) Varieties of Meaning. Mass.: The MIT Press (paperback edition), Cambridge, Millikan, Beyond concepts: unicepts, language, and natural information, Oxford University Press, Oxford UK, 2017, and elsewhere). I argue that the intermediary pragmatics-first approach that I propose, which draws on both Gricean and Millikanian resources, would be better equipped to serve the purposes of those who search for potential precursors of human linguistic communication in animal communication.
 
From Grene (1974, 356). The relation between nature as a whole, material culture, developing human organisms, and “normal’ or “natural” human adults (here “persons”), according to Grene
Article
There are at least two senses in which human beings can be called “naturally artificial”: (1) being adapted for creation of and participation in niche constructed environments, and (2) being adapted for creation of and participation in such environments despite an exceptional indeterminacy in the details of the niche constructed environments themselves. The former puts human beings in a common category with many niche-constructing organisms while the latter is arguably distinctive of our species. I explain how this can be so by developing an account of supporting concepts of complexity, contingency, and content-openness, and show how to defend the position against a common style of objection by a single comparative case study: hermit crabs and their shells versus humans and their movable dwellings. Finally, I consider evidence that such a feature is indeed species-typical and evolved in human populations.
 
Article
Recent philosophical work on causation has focused on distinctions across types of causal relationships. Of the various ways that causal relationships can differ, differences that have been discussed in this literature include stability, specificity, and proportionality (Woodward 2010; Lombrozo et al. 2018). This paper argues for another distinction among causation that has yet to receive attention in this work. This distinction has to do with whether causal relationships have “material continuity” or not, which refers to the reliable movement of material from cause to effect. I provide an analysis of material continuity and argue that causes with this feature (1) are associated with a unique explanatory perspective, (2) are studied with distinct causal investigative methods, and (3) provide different types of causal control over the world.
 
Article
Student learning-centered is intended for mastery of material that demands maximum student abilities through cooperative task completion that is presented in front of classmates. The presentation is being held by a direct discussion of all students guided by groups of presenters and examiners. The research was carried out through a learning process, explorative way purposed of increasing student learning activities. The technique of presenting the assignment results is a debate, that begun by arranging seats in three (3) sections. Two parts face to face and one more part is formed of letter U seats. Learning activities occur when the presenter team presents a material discussion; the examiner team and/or the moderator directly respond and do the rebuttal to review the presenter's material. The audience is invited to give questions and comments to the presenter. The specificity of students' assignments outcomes presentation is a concern of learning process involve the whole aspects of class either the presenter or the all students.
 
A minimal UAL architecture. Unlimited Associative Learning is hypothesized to depend on reciprocal re-entrant connections between sensory, motor, reinforcement and memory processing units, with a central association unit akin to a minimal global workspace at the core of the network. This architecture is proposed to be sufficient for conscious experience. (In Ginsburg and Jablonka 2019, Fig. 8.2, this architecture underlies learning, and therefore includes a specification of the temporal relations between inputs and outputs.)
The global workspace theory. The figure used by Dehaene et al. (1998) to illustrate the core elements of a global workspace. Note that broadcast to a wide range of consumer systems such as planning, reasoning and verbal report does not feature in the figure. © (1998) National Academy of Sciences. The
copyright holder permits non-commercial reuse
Article
This is a response to the nine commentaries on our target article “Unlimited Associative Learning: A primer and some predictions”. Our responses are organized by theme rather than by author. We present a minimal functional architecture for Unlimited Associative Learning (UAL) that aims to tie to together the list of capacities presented in the target article. We explain why we discount higher-order thought (HOT) theories of consciousness. We respond to the criticism that we have overplayed the importance of learning and underplayed the importance of spatial modelling. We decline the invitation to add a negative marker to our proposed positive marker so as to rule out consciousness in plants, but we nonetheless maintain that there is no positive evidence of consciousness in plants. We close by discussing how UAL relates to development and to its material substrate.
 
Uexküll’s model of reciprocal organism-environment interaction. A simplified schema of the ‘function-circle.’ The organism (subject) perceives a ‘carrier of a feature’ of the environment (object) in its ‘perception world’ and reciprocally acts on and shapes the same environment (as a carrier of this effect) in its ‘effect world.’ (After Uexküll 1928:158)
Unknotting organism-environment reciprocal causation. a Organism (O) and environment (E) partake in a loop of reciprocal interaction. b Additional loops represent intrinsic causal processes in the organism and environment. c Organism-environment interactions as in (b) but depicted in a sequential manner. d Model of organism-environment reciprocal causation with a succession of states. Subscripts indicate different states of the organism and the environment, and arrows represent causal contributions. e Application of the model (d) to the case of physical niche construction in reef-building corals. The highlighted arrows and states of corals (O) and their environment (E) constitute a causal path that matches a sequence of steps (1–3) in a causal narrative. For details, see text
Experienced environments and niche construction (I). a Basic model of reciprocal causation between organism (O) and environment (E) including experienced environment (Ex). b Application of the model to an example of constitutive NC, in which the development of a lion (O) changes its experience (Ex) of potential prey in its environment (E). c Example of mediational NC, where the experience (Ex) of low levels of nutrients in the soil (E) causes physiological and developmental changes in a plant (O), which subsequently change the plant’s experience. For the numerated sequence of steps along these paths, see text
Experienced environments and niche construction (II). a Example of relational NC. In a cold nest, mice (O and O’) pile up to change the experience of the temperature of their environment (Ex and Ex’), but not the actual temperature in the nest (E and E’). b Example of relocational NC. Environmental cues (E) cause migration of anadromous fish from the ocean to rivers, during which fish experience (Exτ) different transitional environments (Eτ), out of which the organism chooses one (E’) in which it spawns. See details in the text
Integrating different kinds of niche construction. a Causal diagram of the acceleration of flower production in Solanum melongena (O’) as a consequence of active leaf damage by Bombus terrestris bumblebees (O). Bumblebees’ behavior is triggered by the perceived (Ex) shortage of pollen in the environment (E). Flower production in plants is mediated by their perception (Ex’) of their environment (E’) as threatening. In this case, both organisms are part of each other’s (partly overlapping) environments that causally affect them. b Causal diagram of the transition to herbivory in ruminants (O) in a given environment (E). This transition is partly explained by changes in the rumen (E’) driven by microbes (O’), which cause the animal to experience plants as edible (Ex). For details, see text
Article
In recent years, biologists and philosophers of science have argued that evolutionary theory should incorporate more seriously the idea of ‘reciprocal causation.’ This notion refers to feedback loops whereby organisms change their experiences of the environment or alter the physical properties of their surroundings. In these loops, in particular niche constructing activities are central, since they may alter selection pressures acting on organisms, and thus affect their evolutionary trajectories. This paper discusses long-standing problems that emerge when studying such reciprocal causal processes between organisms and environments. By comparing past approaches to reciprocal causation from the early twentieth century with contemporary ones in niche construction theory, we identify two central reoccurring problems: All of these approaches have not been able to provide a conceptual framework that allows (i) maintaining meaningful boundaries between organisms and environments, instead of merging the two, and (ii) integrating experiential and physical kinds of reciprocal causation. By building on case studies of niche construction research, we provide a model that is able to solve these two problems. It allows distinguishing between mutually interacting organisms and environments in complex scenarios, as well as integrating various forms of experiential and physical niche construction.
 
Article
Niche construction is a concept that captures a wide array of biological phenomena, from the environmental effects of metabolism to the creation of complex structures such as termite mounds and beaver dams. A central point in niche construction theory is that organisms do not just passively undergo developmental, ecological, or evolutionary processes, but are also active participants in them (Lewontin RC, In: DS Bendall (ed) Evolution: From molecules to men, Cambridge University Press, Cambridge, 1983; Laland KN, Odling-Smee J, Feldman MW, In: KN Laland and T Uller (eds) Evolutionary causation: Biological and philosophical reflections, MIT Press, Cambridge, MA, 2019). In this paper, we distinguish between two fundamentally different ways in which organisms are active participants: as agents and as contributors. Roughly, organisms act as agents when niche constructing effects are a result of a goal-directed behavior over which the organisms have some degree of control. Organisms act as contributors when the niche constructing effects do not arise from a goal to perform the constructive activity. As illustrative examples we discuss plants altering leaf-morphology to optimize light exposure as reported by Sultan (Organism and environment: Ecological development, niche construction, and adaptation. Oxford University Press, Oxford, 2015) and bacteria creating novel niches through excreting energy-rich metabolites (San Roman and Wager in PLoS Comput Biol 14: e1006340, 2018). The difference between agential and contributional niche construction is important for understanding the different ways organisms can actively participate in development, ecology, and evolution. Additionally, this distinction can increase our understanding of how the capacity of agency is distributed across the tree of life and how agency influences developmental and evolutionary processes.
 
Article
Birch, Ginsburg, and Jablonka suggest that Unlimited Associative Learning is a “transition marker” in the evolutionary process that produced consciousness, and organizes research by tying together a range of “hallmarks” of consciousness. I argue that the features they recognize as “hallmarks” are indeed important in the evolution of consciousness, but UAL may have a more limited role.
 
The application of networks to GWAS hit prioritisation. In (1), GWAS hits are converted to candidate gene lists. In (2), one selects a cellular network: this could be a gene regulatory network, or a protein-protein interaction network (e.g. from STRING), or a protein-protein regulatory network (possibly constructed via the machine learning methodologies of Invergo et al. (2020)). In (3), genes associated with the GWAS loci are mapped to the chosen network. In (4), network propagation methods (e.g. diffusion techniques) are applied in order identify potential disease-related genes not picked up by the GWAS. In (5), the results of these network analyses are used to identify significant genetic modules to be targeted experimentally in investigations into disease pathogenesis. Note, following Wray et al. (2018) and Barrio-Hernandez et al. (2021), that this particular means of bridging the gap between cellular networks and investigations into the results of GWAS hits does not presuppose a ‘core gene’ hypothesis
Article
It is now well-appreciated by philosophers that contemporary large-scale `-omics' studies in biology stand in non-trivial relationships to more orthodox hypothesis-driven approaches. These relationships have been clarified substantially by Ratti (2015); however, there remains much more to be said regarding how an important field of genomics cited in that work---`genome-wide association studies' (GWAS)---fits into this framework. In the present article, we propose a revision to Ratti's framework more suited to studies such as GWAS. In the process of doing so, we introduce to the philosophical literature novel exploratory experiments in (phospho)proteomics, and demonstrate how these experiments interplay with the above considerations.
 
a Lateral view of spinal cord topography and its different regions: cervical district from C1 to C8, Thoracic district from T1 to T 12, Lumbar district from L1 to L5, Sacral district from S1 to S5 and the Coccygeal segment. Each segment of the spinal cord directly innervates specific regions of skin b and muscle districts c. Reprinted with permission from Springer Nature, Nature Reviews Disease Primers, 3(17,018) Traumatic Spinal Cord Injury, Ahuja et al. (2017)
Article
Within the field of neuroscience, it is assumed that the central nervous system is divided into two functionally distinct components: the brain, which does the cognizing, and the spinal cord, which is a conduit of information enabling the brain to do its job. We dub this the “Cinderella view” of the spinal cord. Here, we suggest it should be abandoned. Marshalling recent empirical findings, we claim that the spinal cord is best conceived as an intrabodily cognitive extension: a piece of biological circuitry that, together with the brain, constitutes our cognitive engine. To do so, after a brief introduction to the anatomy of the spinal cord, we briefly present a number of empirical studies highlighting the role played by the spinal cord in cognitive processing. Having so done, we claim that the spinal cord satisfies two popular and often endorsed criteria used to adjudicate cases of cognitive extension; namely the parity principle and the so-called “trust and glue” criteria. This, we argue, is sufficient to vindicate the role of the spinal cord as an intrabodily mental extension. We then steel our case considering a sizable number of prominent anti-extension arguments, showing that none of them poses a serious threat to our main claim. We then conclude the essay, spelling out a number of far-from trivial implications of our view.
 
Top-cited authors
Derek J. Skillings
  • University of Bordeaux
Joseph A Bulbulia
  • University of Auckland
Ruth Millikan
  • University of Connecticut
Thomas Pradeu
  • French National Centre for Scientific Research
Giovanni Pezzulo
  • Italian National Research Council