Philosophy of Biology

This paper presents an account of the nature of stem cells based on the philosophical concept of disposition. It is argued that stem cells can be conceived as dispositional objects, and adopting this attitude allows overcoming some of the controversies surrounding the nature of stemness (most notably, the state vs. entity debate) because it offers a framework that accommodates the lessons from different theories. Additionally, the account is simultaneously useful for interpreting stem cell experiments and guiding potential interventions. The account (...) shows how different levels, both molecular and emergent network-level, play the primary causal role in explaining some empirical results, and hence they suggest that the explanations can be mechanistic or topological, respectively. The realization that any of these levels may play a more prominent causal role than another allows suggesting interventions at the genetic, molecular and population levels. (shrink)

Open peer commentary on the article “Beyond Individual-Centred 4E Cognition: Systems Biology and Sympoiesis” by Mads Julian Dengsø & Michael David Kirchhoff. Abstract: I concur with Dengsø and Kirchhoff that if we are to ground cognition more deeply in contemporary biology, we need to focus on the organism-environment relationship as the unit of biological explanation most relevant to cognitive science. This entails questioning the individualistic bias that has pervaded 4E cognitive science. However, can we overcome that bias while retaining a (...) commitment to the importance of phenomenological descriptions for 4E cognitive science? Perhaps we can, but probably not if we continue to rely on classical Western phenomenology. Certain strands of Buddhist thought might be more compatible with sympoiesis. (shrink)

The study seeks to contribute to the concept of semiotic causation by building a nomenclature of effects (interpretants) produced by signs. As a starting point, the suggested approach uses Charles Peirce’s idea that the interpretant itself is a sign that is produced by another sign. From this, the study suggests that Peirce’s ten-fold division of signs can be used as a basis for the division of interpretants and, thus, proposes a nomenclature that distinguishes poti-interpretants (interpretants that are quali-signs), sin-interpretants (interpretants (...) that are sin-signs), and legi-interpretants (interpretants that are legi-signs), also differentiating between iconic, indexical, and symbolic interpretants, as well as rhematic, dicent, and argumentive interpretants. The article uses Peirce’s famous whistle example (EP 2:4–5) to illustrate how the proposed systematics of interpretants works and demonstrates that it aligns well with Peirce’s distinction of feeling, reaction, and thinking, as feeling corresponds to the production of iconic poti-interpretants and iconic sin-interpretants, reaction corresponds to the production of indexical sin-interpretants, and thinking corresponds to the production of legi-interpretants. The article also suggests how the proposed ten-fold systematics of interpretants can be reconciled with Peirce’s original classifications of interpretants, as immediate-dynamical-final interpretants correspond to the triad of poti-, sin-, and legi-interpretants, while emotional-energetic-logical interpretants correspond to the three sub-classes of sin-interpretants, i.e. iconic sin-interpretants, rhematic indexical sin-interpretants, and dicent indexical sin-interpretants. The study then explores how the suggested classification of interpretants can be used to draw distinctions between different kinds of semiosis in different agents. In particular, the study shows how the proposed ten-fold classification can be applied to analyze diverse biosemiotic and anthroposemiotic processes. It also tests how different capacities to produce interpretants can be used to distinguish full-fledged signs from quasi-signs and demonstrates that in some cases of zoösemiosis, as well as in proto-semiosis and tardo-semiosis, the production of symbolic interpretants is diminished. (shrink)

Experimental Semiotics (ES) is the study of novel forms of communication that communicators develop in laboratory tasks whose designs prevent them from using language. Thus, ES relates to pragmatics in a “pure,” radical sense, capturing the process of creating the relation between signs and their interpreters as biological, psychological, and social agents. Since such a creation of meaning-making from scratch is of central importance to language evolution research, ES has become the most prolific experimental approach in this field of research. (...) In our paper, we report the results of a study on the scope of recent ES and evaluate the ways in which it is relevant to the study of language origins. We coded for multiple levels across 13 dimensions related to the properties of the emergent communication systems or properties of the study designs, such as type of goal (coordination versus referential), modality of communication, absence or presence of turn-taking, or the presence of vertical vs. horizontal transmission. We discuss our findings and our classification, focusing on the advantages and limitations of those trends in ES, and in particular their ecological validity in the context of bootstrapping communication and the evolution of language. (shrink)

In this commentary, as philosophers of evolutionary biology, we will consider the evolutionary framework used in the Target Article by: (i) emphasising the fruitfulness of the interdisciplinary approach employed; (ii) highlighting some potentially controversial aspects of the proposal; and finally (iii) outlining some ideas for further integration within the UAL framework. The critical analysis will focus on the relationship between learning and consciousness, on the assumed need for a function for consciousness, and on the type of phylogenetic demarcation introduced by (...) UAL. (shrink)

Human music and language are two systems of communication and expression that, while historically considered to overlap, have become increasingly divergent in their approach and study. Music and language almost certainly co-evolved and emerged from the same semiotic field, and this relationship as well as co-origin are actively researched and debated. For the sake of evaluating the semiotic content of zoomusicology, we investigate music from a ‘bottom-up’ biosemiotic functionalist account considering iconic, indexical, and symbolic forms of meaning not in a (...) hierarchy but according to their effects on agents. Such an approach avoids overintellectualizing the representational aspects of music, and instead inverts, as it were, the traditional hierarchy of semiotic categories to produce illocutionary effects. Understanding aesthetics and action not as a priori separate but rather fundamentally co-arising elements of the same events. The focus of musicality again returns to interpretation and how semiosis precipitates expression. (shrink)

The ability of predicting upcoming events or conditions in advance offers substantial selective advantage to living beings. The most successful systematic tool for fairly reliable prognoses is the use of dynamical causal models in combination with memorised experience. Surprisingly, causality is a fundamental but rather controversially disputed concept. For both models and memory, symbol processing is requisite. Symbols are a necessary and sufficient attribute of life from its very beginning; the process of their evolutionary emergence was discovered by Julian Huxley (...) a century ago. In behavioural biology, this universal symmetry-breaking kinetic phase transition became known as ritualisation. Symbol use for predicting future dynamical processes has culminated in the unprecedented complexity of mental models used in science and technology, coining the historical ascent of modern humans. Observation and measurement transform structural information of physical exchange processes into symbolic information from which state quantities are derived by means of mental models. However, phylogenetically inherited models such as naïve realism do not necessarily explain the sophisticated insights revealed by modern experiments with, say, entangled quantum states. It is suggested to carefully distinguish observed exchange quantities from predicted unobservable state quantities, and physical reality from mental models thereof. (shrink)

Species conservation activities are gaining more attention in the context of environmental degradation. This article proposes to tackle different semiotic aspects of reintroduction as one possible way of furthering species conservation. More specifically, we aim to bring forth the strength of ecosemiotic perspective when dealing with such a complex matter with many different human and non-human subjects. We concentrate on animal agency, search and function tone, semiotic fitting and changes in umwelten when analysing the reintroduction process from the perspective of (...) the animal. When considering the locals’ perspective, we take into account the appeal and cultural placement of the species, as well as human and non-human umwelt overlap when it comes to resources. As our case study we use the European mink (Mustela lutreola) and its reintroduction to the island of Hiiumaa and planned reintroduction to the island of Saaremaa in Estonia. By employing semiotic analysis, we discover that reintroduced animals need to exhibit innovation and plasticity to establish novel semiotic relations but also restore relations characteristic to the historical environments of the species. We argue that human views and expectations towards the species and (re)introduction efforts account for animals’ appearance and agency. Additionally, contrast with other wild species, the perceived overlap of human and non-human umwelten, and broader conservation discourse are decisive for the formation of interspecific relations in situ. Thus, ecosemiotcs proves to be a valuable research platform for an analysis of conservation practices that targets both, sociocultural context and animal umwelten. (shrink)

Life has evolved; and so must have consciousness, or subjective experience, as found in living beings, Eva Jablonka and Simona Ginsburg contend. In their target article, which summarises the main theses of their seminal book The Evolution of the Sensitive Soul, the authors put forward an evolutionary account of consciousness that builds upon the intimate connection between consciousness and life without, however, equating the two. Instead, according to Jablonka & Ginsburg, there was life before there was consciousness, and there are (...) still living beings without consciousness. Here I offer some metaphysical considerations in favour of a more inclusive notion of consciousness than Jablonka & Ginsburg’s. These considerations turn on the role played by metabolism and agency in the processual constitution of living beings as well as on the continuum between sensation and perception. Rather than postulating a mindless inwardness in presumably non-conscious organisms, we ought to recognise the constitutive experiential nature of life, rooted in its intrinsic purposiveness. (shrink)

Jablonka and Ginsburg’s target paper (2022) argues that (a) consciousness is closely tied to goal-directed behavior and an open-ended capacity for learning and adaptation driven by exploration-and-stabilization dynamics; and (b) consciousness has this essential dynamical nature due to its emergence in evolution from the spontaneous exploration-and-stabilization dynamics of animal life, which the authors term vivaciousness. In this commentary, I explore these two claims with relation to two features of experience that are of clear importance to goal-directed behavior both phenomenologically and (...) biologically: (1) the role of probabilistic expectation, and (2) the role of available energy. Applying Jablonka and Ginsburg’s framework, I argue that these two features are substantive and potentially universal examples of consciousness being shaped by biology. (shrink)

The abstract basis of modern computation is the formal description of a finite state machine, the Universal Turing Machine, based on manipulation of integers and logic symbols. In this contribution to the discourse on the computer-brain analogy, we discuss the extent to which analog computing, as performed by the mammalian brain, is like and unlike the digital computing of Universal Turing Machines. We begin with ordinary reality being a permanent dialog between continuous and discontinuous worlds. So it is with computing, (...) which can be analog or digital, and is often mixed. The theory behind computers is essentially digital, but efficient simulations of phenomena can be performed by analog devices; indeed, any physical calculation requires implementation in the physical world and is therefore analog to some extent, despite being based on abstract logic and arithmetic. The mammalian brain, comprised of neuronal networks, functions as an analog device and has given rise to artificial neural networks that are implemented as digital algorithms but function as analog models would. Analog constructs compute with the implementation of a variety of feedback and feedforward loops. In contrast, digital algorithms allow the implementation of recursive processes that enable them to generate unparalleled emergent properties. We briefly illustrate how the cortical organization of neurons can integrate signals and make predictions analogically. While we conclude that brains are not digital computers, we speculate on the recent implementation of human writing in the brain as a possible digital path that slowly evolves the brain into a genuine (slow) Turing machine. (shrink)

Pasteur’s originality in the way he developed pure research is to have understood the importance, for society, of the underlying motivation. Curiosity, of course, is a strong motivation, which explains why we seek to understand the origin of life. But, in front of the immensity of the possible choices, why not, also, choose to start from questions of economic interest (diseases of beer and wine, diseases aVecting the silk industry . . . ) Finally, of course, health is a constant (...) preoccupation, but the diseases, which have no borders, often come from tropical countries and Asia especially. It is therefore necessary to settle there, but not to come and impose one’s point of view, but on the contrary to use the knowledge coming from the local culture in order to open new ways of understanding the reality of the world. (shrink)

Human interaction with the living world, in science and beyond, always involves classification. While it has been a long-standing scientific goal to produce a single all-purpose taxonomy of life to cater for this need, classificatory practice is often subject to confusion and disagreement, and many philosophers have advocated forms of classificatory pluralism. This entails that multiple classifications should be allowed to coexist, and that whichever classification is best, is context-dependent. In this paper, we discuss some practical consequences of classificatory pluralism, (...) in particular with regard to how one is supposed to find the best classification for a given context. We do so by means of a case study concerning oaks, in particular the pedunculate oak (_Quercus robur_ L.) and the sessile oak (_Quercus petraea_ (Matt.) Liebl.), two important putative species that present several classificatory challenges; and by applying one recent philosophical framework conceptualizing classification, the so-called Grounded Functionality Account (GFA) of (natural) kinds. We show how the GFA elucidates several issues related to oak classification and gives directions to optimize classificatory practices, and discuss some implications for scientific taxonomy. (shrink)

A long-standing problem in understanding goal-directed systems has been the insufficiency of mechanistic explanations to make sense of them. This paper offers a solution to this problem. It begins by observing the limitations of mechanistic decompositions when it comes to understanding physical fields. We argue that introducing the field concept, as it has been developed in field theory, alongside mechanisms is able to provide an account of goal directedness in the sciences.

A recent idea of “ecosystem health” was introduced in the 1970s and 1980s to draws attention to the fact that ecosystems can become ill because of a reduction of properties such as primary productivity, functions and diversity of interactions among system components. Starting from the 1990s, this idea has been deeply criticized by authors who argued that, insofar as ecosystems show many differences with respect to organismic features, these two kinds of systems cannot share a typical organismic property such as (...) health. In recent years, an organisational approach in philosophy of biology and ecology argued that both organisms and ecosystems may share a fundamental characteristic despite their differences, namely, organisational closure. Based on this kind of closure, scholars have also discussed health and malfunctional states in organisms. In this paper, we examine the possibility of expanding such an organisational approach to health and malfunctions to the ecological domain. Firstly, we will see that a malfunction is related to a lower effectiveness in the functional behaviour of some biotic components with respect to other systemic components. We will then show how some introduced species do not satisfactorily interact in an organisational closure with other ecosystem components, thus posing a threat to the self-maintenance of the ecosystem in which they are found. Accordingly, we will argue that an ecosystem can be said to be healthy when it is a vital environment organisationally grounded on its intrinsic capacity to ensure, under favourable conditions, appropriate functional behaviours for ecosystem components and ecosystem self-maintenance. (shrink)

In this article, in an attempt to analyze the crisis caused by the images of imported plastic waste, we consider the relationship between waste and its meaning in the case of geographical dislocation and de- and re-contextualization processes. Our analysis is guided by two recent concepts: The Wasteocene and semiocide. While the Wasteocene clarifies the signifying mechanisms of this period, semiocide allows us to understand which signs, under what conditions, are rendered invisible or disregardable. In coining the concept of semiocide, (...) Ivar Puura emphasized two key features of the phenomenon. Following this distinction, which is based on (un)intentionality, semiocide refers either to a fully conscious, perhaps even hostile, attempt to destroy a semiotic configuration, or to a completely nonconscious, unaware process in which the unawareness itself is the source of the destruction. Although a more cultural approach dominates in Puura’s assertion of the concept, the concept is applicable to human classification, interpretation and transformation of nature (Maran, 2013; Tønnessen et al., 2015). Focusing on the case of Adana as a recent example of a global waste crisis, our aim is to provide a (bio)semiotic framework for assessing how and under what conditions plastic materials become arbiters of environmental and political crises. With heaps of plastic garbage with foreign names on them, the discourse of recycling, restricted media coverage, public indignation, the struggles of environmentalist organizations, and the encounter of different spatio-temporalities, our study aims to convey an impoverished narrative of a city in the south of Türkiye. (shrink)

Since their introduction in Colombia in the '80s for Pablo Escobar’s extravagant zoo, hippos have become an ecological problem around the basin of the Magdalena River. This article proposes an ecosemiotic discourse analysis of different visions of nature enacted by stakeholders and public opinion around the management of hippos in Colombia. Concretely, we focus on three particular discourses and visions of nature: animalista, narco-cultural, and conservacionista. In this article, we present the relevant social and ecological context of Colombia, the visions (...) of nature theory and the impact of such visions on conservation measures regarding so-called invasive species; we describe and analyze the three visions of nature we center on, and present a computational analysis of discourse dynamics and controversies in Twitter between of such visions of nature; and we reflect on possible courses of action and recommendations about addressing the close interrelation of public discourses and ecosystem conservation by proposing an alternative view, based on the biosemiotic framework of semiocide, to the concept of invasive species. (shrink)

We argue that Madole & Harden's distinction between shallow versus deep genetic causes can bring some clarity to causal claims arising from genome-wide association studies (GWASs). However, the authors argue that GWAS only finds shallow genetic causes, making GWAS commensurate with the environmental studies they hope to supplant. We also assess whether their distinction applies best to explanations or causes.

I offer a defense, albeit a qualified one, of machine analogies in biology, focusing on molecular contexts. The defense is rooted in my prior work (Levy in Philosopher’s Imprint 14(6), 2014), which construes the machine machine-likeness of a system as a matter of the extent to which it exhibits an internal division of labor. A concrete aim is to shore up the notion of molecular biological machines, paying special attention to processive molecular motors, such as Kinesin. But I will also (...) try to show how the division of labor account gives us guidance more broadly, both about where and why machine analogies can be expected to prove helpful and about their limitations. (shrink)

In this article two questions are discussed with regard to semiosis in protein biosynthesis for nano engines. (1) What kind of semiosis is involved in the construction of these proteins? and (2) How can we explain the semiotic process observed? With regard to the first issue we draw attention to comparisons between semiosis in protein biosynthesis and human natural language. The notion of normativity appears to be of great importance for both. A comparison also demonstrates differences. Nevertheless, because of the (...) normative symbolic information processing in it, we suggest to employ the term symbolic reference (employed in linguistics as a distinguishing feature of human language) to indicate the semiotic processes in protein biosynthesis. With regard to explaining semiosis in protein synthesis we compare different approaches. We conclude that a Kantian approach should be preferred. In such an approach strengths of the mechanistic and organicist approaches can be combined, and the observed symbolic information processing acknowledged. (shrink)

In his Ecolinguistics, Stibbe (2020) declares the story of economic growth (the continuous increase in production and consumption) as the ‘master narrative’ that is at the same time the most harmful story we live by. This paper explains where this story of growth comes from and describes how it supplants or suppresses alternatives, such as stories of thrift and sharing. By connecting the biosemiotic model of Funktionskreis (e.g. Uexküll, 1920) as “the primary mechanism of meaning making” (Kull 2020) to cognitive (...) linguistics (e.g. Lakoff, 2009) and critical discourse analysis (e.g. van Leeuwen, 2018), this paper explores how stories of thrift and sharing can be turned into activism that seeks to reframe waste as surplus that can be shared; but they can also hide the old business models of the master narrative. Stories of sharing are often erased to protect corporate interests. Narratives of sharing can be duplicitous, especially in the context of the ‘sharing economy’. Attempts at reframing resources and energy as common wealth owned by everyone are squelched by the master narrative in contexts like resource and energy distribution. Can the new story of shrinking and degrowth become a new alternative to the master narrative and promote new decelerated semiotic habits (Maran, 2023) for a more fulfilling life with less (e.g. Herrmann 2022)? (shrink)

Understanding how biological organisms are autonomous—maintain themselves far from equilibrium through their own activities—requires understanding how they regulate those activities. In multicellular animals, such control can be exercised either via endocrine signaling through the vasculature or via neurons. In C. elegans this control is exercised by a well-delineated relatively small but distributed nervous system that relies on both chemical and electric transmission of signals. This system provides resources to integrate information from multiple sources as needed to maintain the organism. Especially (...) important for the exercise of neural control are neuromodulators, which we present as setting agendas for control through more traditional electrical signaling. To illustrate how the C. elegans nervous system integrates multiple sources of information in controlling activities important for autonomy, we focus on feeding behavior and responses to adverse conditions. We conclude by considering how a distributed nervous system without a centralized controller is nonetheless adequate for autonomy. (shrink)

Targeted hypermutation has proven to be a useful survival strategy for bacteria under severe stress and is also used by multicellular organisms in specific instances such as the mammalian immune system. This might appear surprising, given the generally observed deleterious effects of poor replication fidelity/high mutation rate. A previous theoretical model designed to explore the role of replication fidelity in the origin of life was applied to a simulated hypermutation scenario. The results confirmed that the same model is useful for (...) analyzing hypermutation and can predict the effects of the same parameters (survival probability, replication fidelity, mutation effect, and others) on the survival of cellular populations undergoing hypermutation as a result of severe stress. (shrink)

This chapter argues that a Peircean philosophy of sex offers a non-reductionist approach to sex as a biological category. The chapter surveys traditional biological accounts of sex categories and several social constructivist accounts of sex. It then provides an overview of Peirce’s scholastic realism and his ethics of inquiry. While Peirce regarded the distinction between the sexes as a rare “polar distinction”, the chapter works to recover the nuanced view of sex that Peirce ought to have adopted had he extended (...) his scholastic realism to reproductive biology. Ultimately, the Peircean account offered treats sex differences as norms expressed as bimodal distributions. The chapter concludes by illustrating some applications of this Peircean philosophy of sex, and gesturing to those that we can yet barely imagine. (shrink)