Philosophy of Biology

Information from our senses, memories and thoughts is bound together into a unified whole that constitutes our experience of our world, our Umwelt. However, our ability to investigate our Umwelt through standard Western-derived neuroscience is limited, because of the third-person approach that undergirds the field. Achieving greater coherence in our understanding requires the addition of an approach which is fundamentally integrative. The most comprehensive first-person approach to the nervous system can be found in the introspective traditions of Tantric Hinduism. In (...) this review, we explore the hierarchical ordering of the senses in Hinduism (from most gross to the most subtle, the latter being closer to consciousness), and how this may be linked to sensorimotor coupling in the parietal cortex. We demonstrate how this ordering parallels the developmental history of the sensory cortices over the course of vertebrate evolution. The synergy between biosemiotics and neurophenomenology is made clear, as the idea of a “Great Chain of Semiosis” can be very helpful in understanding the reasons behind the emergence of this sensory hierarchy. The structures of the Subtle body described in Hindu Tantra should be seen as semiotic nodes used by the conscious agent in interacting with the world around it. We propose that metaphor ties together the various sensory mappings of the body at the cognitive level. Integrating insights from Hindu Tantra will help modern science better investigate questions of agency, meaning and semiosis in organisms. (shrink)

Conflicts within the tsetse fly belt revealed a strong correlation between the dynamics of bovine trypanosomosis and the insurgency involving farmers and herders in Nigeria and parts of West Africa. This study examined the history, causes and influence of farmers-herdsmen conflicts on banditry, terrorism and food security as it relates to the epidemiology of African animal trypanosomosis (AAT). A combination of literature database searches, semi-structured questionnaires, and mathematical modeling was employed. The study found that transhumance contributes significantly to conflicts between (...) farmers and herdsmen. An average of 6.46 persons per attack were reported between 2005 and 2021. Only 8.4 $$\%$$ (95 $$\%$$ CI: 5.0 $$-$$ 12.9) of farmers and 18.2 $$\%$$ (95 $$\%$$ CI: 12.4 $$-$$ 25.4) of herdsmen have engaged in conflict resolution efforts. The study shows that both conflict and the spread of trypanosomosis can be effectively controlled when $$R_0 < 1$$, ensuring that the sub-population remains in the basin of attraction of the trypanosomosis-conflict-free equilibrium ( $$T_{0c}$$ ). The partial derivative of the basic reproduction number, $$R_0$$, with respect to improved conflict resolution, suggests that halting transhumance can prevent a portion of the cattle recruitment rate ( $$\Lambda_c$$ ) from becoming infected with AAT. Climate change exacerbates these issues, leading to settlement and resettlement strategies within the fly belt regions. The model indicates that the basic reproduction number can only be reduced to less than one ( $$R_0 < 1$$ ) to become globally asymptotically stable if there is effective conflict resolution involving both farmers and herders. The study advocates for the establishment of ranching in tsetse-free zones with adequate social amenities, improved marketing strategies for animals and animal products led by government agencies through public-private partnerships, the banning of open grazing, and strict enforcement of policies against violators. (shrink)

We revisit John Worrall’s old but still prominent argument against the view that randomization balances the impact of both known and unknown confounders across the treatment and control arms. We argue that his argument involving indefinitely many possible confounders is at odds with statistical theory as it (1) presumes that the purpose of randomized studies is obtaining perfect point estimates for which perfect balance is needed; (2) mistakes equalizing each confounder with the overall (average) impact of all confounders, and (3) (...) assumes that the joint effect of an infinite series of confounders cannot be bounded. We defend the role of randomization in balancing the impact of confounders across the treatment and control arms by putting forward the statistical sense of the balance claim. It involves the following three commitments: (1) randomization balances confounders in expectancy, (2) for RCTs to deliver unbiased estimates of the causal effect (true average treatment effect), the balance in the average effect of all confounders and not balancing each confounder is sufficient, and (3) randomization allows for calculating the probability of deviating from the balance. The paper includes a review of how the balance claim has been understood so far and discusses recent arguments supporting randomization balancing the impact of confounders in expectancy and the crucial role of the average impact of all actual confounders, and shows how statistical analysis of RCTs conducted both at the design and analysis stage makes possible estimating the probabilities of deviating from the balance. (shrink)

The selected effects theory is supposed to provide a fully naturalistic basis for statements about what biological traits or processes are for without appeal to final causes or intelligent design. On the selected effects theory, biologists are allowed to say, for instance, that hindwing eyespots on butterfly wings serve to deflect predators’ attacks away from vital organs because a similar fitness-enhancing effect explains why eyespots themselves were favoured by natural selection and persisted in the population. This is known as the (...) explanatory dimension of the selected effects theory. According to it, appealing to the fitness-enhancing effect of a certain trait or process is sufficient to explain its current presence in a population, namely, why it persisted and still exists in that population. In this paper, however, I will call such a claim into question, and I will do so by discussing a mathematical Hawk-Dove example and a real case scenario taken from evolutionary biology, that of Perissodus microlepis. These are scenarios in which the selective filter does not allow variants with the highest fitness at a certain moment to prevail over their available alternatives. In similar cases, I will argue, citing fitness-enhancing effects does not represent an adequate explanation of what happens in the population, undermining the explanatory dimension of the selected effects theory. (shrink)

The article presents and critically discusses the concept of environmental interventionism, which treats interference in the functioning of ecosystems to protect free-living animals from suffering as a general ethical obligation. The strong version of this approach postulates the need to help animals suffering from natural phenomena, and the extreme version recommends the permanent reconstruction of animal bodies using biotechnology. The dispute between proponents and opponents of this concept can be reduced to a fundamental dispute over the primacy of two sets (...) of ethical values: the individual values of particular animals, characteristic of the animal welfare stance, and the values attached to the supra-individual manifestations of the biosphere, characteristic of the environmentalist ethic. The arguments presented in the article justify the application of the principles of environmental ethics in order to protect the biosphere against the contemporary ecological crisis and clearly result from Author’s full acceptance of the assumptions of ethical naturalism. The paper attempts to show that the arguments for the validity of interventionism are based on partially erroneous assumptions and questionable conclusions. These include: ignoring knowledge of the advanced cognitive abilities of many groups of animals and their implications for ethical obligations towards them; clinging to an archaic, individualistic vision of the functioning of the biosphere; super-naturalising the approach to individual suffering; and making an unjustified transfer between intrinsic and instrumental values ascribed to animals. By basing the hierarchy of animals and their life interests used to prioritize interventionism on the arbitrary opinions of humans, this concept is clearly anthropocentric. The article presents arguments for recognising the strong and extreme version of instrumentalism as harmful from the point of view of environmental ethics and biosphere protection. (shrink)

We discuss how biosemiotics sheds light on a problem that characterizes the social reproduction system today in globalisation, how social and political systems threaten life on the planet. These reflections engage global semiotics developed as semioethics where “ethics” resounds as entanglement in the I-other relation. Like medical semeiotic at the origin of semiotics, semioethics elects life as a primary value. Biosemiotics reveals the condition of interconnectivity, co-implication, interdependency among all lifeforms. As such it is an important reference for semioethics which (...) in turn underlines how life in the social, political, economic and broadly cultural spheres is subject to the biological, thus how values, ideologies and responsibilities enter the same great semiobiosphere where bodies and signs are co-dependent and respond to each other in semiosis. Central notions for signs and society are questioned in this framework, firstly humanism of identity. I-other entanglement is global, the condition for life to flourish. Challenged by human and ecological emergency, semioethics considers the biocultural implications and appeals to global responsibility. (shrink)

Virtual reality allows participants to experience immersive perspective-taking which is key to stimulate empathy and emotion sharedness. Immersive interaction performed by the participants is examined in this article as an experience of cultural embodiment. Following a biosemiotic approach to culture, the study examines the virtual reality movie Waves of Grace qualitatively. It seeks to trace how participants’ interaction with the virtual worlds elicits in them a feeling of being embodied in a world of Ebola suffering that is outside the cultural (...) paradigm of their real world. Biosemiotics provides a theoretical platform which helps in deconstructing the complexity of participants’ kinetic interactions within both physical and virtual spaces, and, in a way, reconstructing the concept of cultural embodiment. Correspondingly, the analysis yields that cultural embodiment is instantiated through kinetic movement and rhythmical interaction where participants are not only told about the story of Ebola but inhabit its umwelt and reconfigure it. Enacting an umwelt-to-umwelt interaction, participants not only alter the visual scenes and affect their affordances, but they also model subjective worlds that scaffold how they feel, and how they relate to the virtual situation. The findings suggest to update the metaphors used to understand the ‘viewing’ of suffering and sufferers (most notably among them is spectatorship of suffering and distant suffering). The world of suffering is embodied rather than communicated. The article makes a contribution to biosemiotic cultural studies by introducing the concept of physical-virtual kinetic rhythms to the notion of cultural embodiment. (shrink)

This paper aims to understand how and why tree diagrams are of central importance to microbiome scientists in their practices of meaning making. The interfaces that scientists use are, in fact, topological structures that organize the genetic data generated by sequencing technology. They establish relationships among microbes and also between microbes and the conditions of the ecological niche they help construct. The tree structure is a powerful _topos_ of knowledge organization in Western culture. However, biomolecular research has revealed the existence (...) of horizontal gene exchange among microbes and other merging forms; these cast doubt on the tree as a valid representational metaphor for the tangle of the microbial world and help to overcome neo-Darwinism. This essay analyzes the software and interfaces used by microbiome scientists as tools for organizing knowledge that shape how we see human-microbe relationships, while escaping a representational function. While trees have long been considered representative forms of visualization of an evolutionary paradigm, we emphasize the non-illustrative and heuristic power of these interfaces, which, although steeped in centuries of reflection and debate on evolutionary theories, respond more to a diagrammatic logic: tools for discovering the new from genetic “black matter” and for exploring new forms of relationships between microbes and humans. (shrink)

The article investigates basic relations between aesthetics and communication based on studies of and discussions about what has been termed “animal beauty”. The concepts _beauty_, _aesthetics_, and _communication_ are problematised, starting from utterances’ _structured form_, which is seen both as the physical basis for as well as one of five key aspects in animal utterances (form, content, act, time, and space). The relational, and thus social semiotic, communicational role of this aspect is searched in different studies leading to two major (...) claims: Firstly, that five corresponding constitutional traits or _aspects_, aesthetics, epistemology, ethics, temporality, and spatiality collectively form a basis for animals’ evaluation of the subjective _value_ of utterances. The importance of each of them varies depending on what _kind_ of communication (life-genre) they are associated with. Secondly, that aesthetics should be comprehended on four integrated _levels_, from micro to macro, sign, utterance, life-genre, and life-world. These four levels plus five aspects or components in utterances make up a systemic, social semiotic communicational framework which in turn is applied for inspections of studies studying “beauty”. Methodological challenges applying them are briefly discussed. An overall conclusion is that research on the evolutionary role of animal beauty should treat the aesthetics of utterances as part of the hermeneutic circle, simultaneously as categorial _and_ relational, in other words as a constitutive part of a whole, a semiotic, species-specific socio-communicational system. (shrink)

This article reexamines meaning, agency, and interpretation by challenging the view that they require primary or secondary agency. Using Paul Ricœur’s narrative temporality, it explores Terrence Deacon’s autogenic theory, reinterpreting it as a narrative process with non-agentic meaning by distinguishing between distended and displaced temporal relations. Distended relations pertain to agency and biosemiosis, while displaced relations involve the meaning found not in the entity but the processes which gave it a functionally historicized existence. Applying Ricœur’s analysis of temporal aporia and (...) Deacon’s concept of zero, the article suggests that meaning in Deacon’s model mirrors the normative process of narrative interpretation. It emphasizes that primary agency requires meaningful organization for agentic action to have a self for which decisions matter, concluding that meaning, life, and primary agency are grounded in already existing displaced temporal relations resultant from proto-interpretative relations not bounded within an organism. (shrink)

Sex is fundamental to many organisms. It is through sexual reproduction that humans, and many metazoans (multicellular eukaryotes in the animal kingdom), propagate our species. For more than 150 years, sexual reproduction within metazoans has been understood to rely on the existence of a discrete category of cells (germ cells) that are usually considered uniquely separate from all other cells in the body (somatic cells), and which form a cell lineage (germline) that is sequestered from all somatic cell lineages. The (...) consideration of germ cells and germline as the lone source of reproductive potential within metazoans has allowed many investigators to place the hereditary and evolutionary burdens of sexually reproducing lineages solely within these cells and cell lineages, making them central to many important topics within biology, such as units of selection, transmission and population genetics, Darwinian evolution, and individuality. Regarding these topics, there is a predominant and shared understanding of germ cells, somatic cells, and the ways in which these two relate to each other that is rarely critically evaluated. In this article, I lay out how germ cells and germline within metazoans are understood by a majority of scientists and philosophers, both now and historically, by sketching out what I call the predominant epistemic framework of germ. I show how this framework conflicts with empirical evidence, propose a series of revisions to realign it with this evidence, and indicate why such revisions are urgently needed by highlighting the case of somatic cell genome editing. (shrink)

The organism is the central entity in biological science. However, consensus with regard to the definition of the underlying concept is lacking. Moreover, several ambiguous life forms exist that challenge current definitions of the term. Based on a comprehensive analysis of the available literature, we provide an overview of the criteria and approaches that have been previously used to define organismality. In addition, we highlight non-paradigmatic biological entities to identify problems that challenge definitions of organismal units. To address these issues, (...) we propose a cross-disciplinary definition of the organism concept and provide a list of key criteria that allow both paradigmatic and non-paradigmatic cases to be unequivocally classified. In this way, our work not only provides newcomers with an overview of this exciting field, but also enhances communication across disciplines. (shrink)

In recent years the study of well-being has attracted considerable attention, fostering hope that the scientific community will ultimately succeed in discovering its very nature, thereby emulating successful scientific projects in other disciplines. However, there have been recurring worries about how to measure and define well-being. In this context, Hersch (Br J Philos Sci 73:1045–1065, 2022) has recently argued that we could progressively alleviate these worries through an iterative dialogue between theory and measurement, by seeing them as stemming from a (...) coordination problem. In this article, I argue that the concept of well-being fails to meet the prerequisites for Hersch’s approach. If the latter is the best defense of the capacity of science to uncover the nature of well-being, it follows that the science of well-being should probably relinquish this ambition. (shrink)

The goal of this paper is to explore a set of epistemological and ontological issues regarding the historical and philosophical role of placebos in the contested history of antidepressants. Starting from an account of the dual nature of the placebo as both an epistemic and a therapeutic tool, and against the background of the heated debates on the efficacy of second-generation antidepressants, I propose two related arguments. First, I argue that placebos as controls played a crucial but paradoxical role in (...) the rise of so-called evidence-based approaches to depression. Second, I discuss how current research on placebo effects puts into question some of the most crucial assumptions of psychiatric technoscience regarding the ontology of affective experiences. Ultimately, this paper aims to probe discussions around placebos, placebo effects, and the status of depression both as a diagnostic category and a lived experience. (shrink)

Life cycle diagrams are ubiquitous in a variety of scientific materials, ranging from introductory biology textbooks to professional publications. These diagrams typically depict stages of a particular organism’s life connected by arrows, such as, for a frog: egg(s) → embryo → tadpole → tadpole with two legs → tadpole with four legs → young frog → adult frog → egg(s). In this paper, we present a critique of this sort of life cycle diagram, drawing on both metaphysics and epistemology of (...) science. We suggest that these diagrams do not accurately represent an organism’s life stages, its reproduction, or species persistence. These misrepresentations have implications for scientific reasoning, explanatory efficacy, as well as pedagogical efficacy. To address the shortcomings of these diagrams, we propose a new kind of diagram which we call the life spiral diagram. The life spiral diagram more accurately reflects an organism’s life stages, its reproduction, as well as species persistence. Thus, the life spiral diagram better aids scientific reasoning, explanations of life processes, and learning. (shrink)

In this paper, we consider whether a straightforward answer can be provided to the following question regarding function ascriptions in genome biology: when does the activity of a genomic segment become functional or, perhaps, fully functional? We respond by examining de novo explanatory models for the emergence of genes, i.e., functional genomic entities. Our case study is especially pertinent to discussions about genome functionality, because what is meant by function, then, is crucial in assessing what constitutes a de novo gene (...) origination. We show that, according to these models, there is no single point at which a genome segment acquires functionality. On the contrary, there is a continuum going from non-functional, through proto-functional, to fully functional. This suggests a gradational functionality for genomic objects, instead of an all-or-nothing one, as implied by standard views in the debate on biological functions. It has recently been argued by Matthewson (Biology Philos 35:4, 2020) that proper functions come in degrees because natural selection comes in degrees. We extend that argument and show that the continuum of functionality or, at least, proto-functionality, can be applied to genomic segments even before they are under the influence of natural selection. Accordingly, we argue that a weak etiological account is most suitable for capturing the phenomenon of new biological functions arising at the genomic level. (shrink)

A Comparative Analysis of the similarities between longevity in Koi and Empires.

Charbonneau ( 2014 ) and Papale ( 2021 ) challenge the necessity of reproduction for evolution by natural selection (ENS) by contending that what really matter for ENS are memory and (re)generation at the population level, rather than lineage-forming reproduction at the local level. In this article, we critically evaluate their reproduction-independent accounts of ENS and defend the importance of lineage-forming reproduction in paradigmatic ENS on both empirical and theoretical grounds. We argue that none of the empirical cases they cite (...) can be used as evidence to demonstrate the existence of paradigmatic ENS without lineage-forming reproduction, and adopting their reproduction-independent views would lead to an account of ENS that is both too liberal and too strict. (shrink)

The pursuit of science is a specific form of cognitive activity that is guided by concrete heuristic objectives and corresponding standards in terms of its methodological approach. The philosophy of science pursues the goal of analyzing scientific cognitive activity against the background of epistemology. The core problem of traditional philosophical epistemology, and with it the current philosophy of science, according to my thesis, consists in the heuristic short-circuiting of the content with the object of knowledge. This manifests itself directly in (...) its focus on the heuristic standard of certainty of our knowledge, based on the metaphysical assumption of the determinacy of things in themselves (which correlates with the supposition of the mode of description as the paradigm of cognitive activity in general). The main thesis of this paper will be that this short-circuit leads to a suppression of the role of heuristics as a fundamental factor of cognitive activity, and in its consequence to a descriptive misunderstanding of the deconstructive mathematical heuristic of physics (with its focus on dynamical phenomena) in terms of mere decomposition. Owing to the role of physics as a fundamental science, the consequences of this misunderstanding are far-reaching. Particularly for the scientific self-understanding of biology, namely in the sense of the heuristic goal of analytically decomposing biological entities into physical ones and reducing biological phenomena to physical laws. This goal clearly contradicts the deconstructive methodological approach of physics, whose only yardstick is the appropriateness of the reconstruction of the phenomena under consideration. (shrink)

Das Betreiben von Wissenschaft ist eine spezifische Form von Erkenntnistätigkeit, die bezüglich ihrer methodischen Vorgangsweise von konkreten heuristischen Zielsetzungen und korrespondierenden Maßstäben geleitet ist. Die Wissenschaftstheorie verfolgt das Ziel einer Analyse der wissenschaftlichen Erkenntnistätigkeit vor dem Hintergrund der Erkenntnistheorie. Das Kernproblem der traditionellen philosophischen Erkenntnistheorie, und mit ihr der gängigen Wissenschaftstheorie, so meine These, besteht in dem heuristischen Kurzschluss des Inhalts mit dem Gegenstand der Erkenntnis. Dieser manifestiert sich auf direkte Weise in ihrem Fokus auf den heuristischen Maßstab der Gewissheit (...) unseres Wissens, gestützt auf die metaphysische Annahme der Bestimmtheit der Dinge an sich (der die Annahme von Deskription als Paradigma von Erkenntnis im allgemeinen korrepondiert). Die Hauptthese dieser Abhandlung wird sein, dass dieser Kurzschluss zu einer Ausblendung der Rolle der Heuristik als grundlegender Erkenntnisfaktor führt, und in seiner Konsequenz zum deskriptiven Missverständnis der dekonstruktiven mathematischen Heuristik der Physik (mit ihrem Fokus auf die dynamnischen Phänomene) im Sinne von bloßer Dekomposition. Die Folgen dieses Missverständnisses sind, der Rolle der Physik als Grundlagenwissenschaft geschuldet, weitreichend. Insbesondere für das wissenschaftliche Selbstverständnis der Biologie, im Sinne des Ziels, biologische Entitäten analytisch in physikalische zu zerlegen und biologische Phänomene auf physikalische Gesetze zu reduzieren. Dieses Ziel widerspricht klar der dekonstruktiven methodischen Vorgangsweise der Physik, deren einziger Maßstab in der Angemessenheit der Rekonstruktion der betreffenden Phänomene besteht. (shrink)

The evolutionary emergence of consciousness is a research topic that has been attracting increasing attention in recent years. In a brief span of time, the debate surrounding various models in this area is driving the development of an increasingly specific research agenda. In this article, we examine the main available models of emergence. All the models we discuss assume, with varying degrees of caution, that consciousness emerged through convergent evolution in three distinct phyla within the animal kingdom. Nevertheless, they provide (...) a unified account that aims to comprehensively cover all independent tokens of emergence. After analyzing the suitability of this unifying strategy through the lens of contemporary evolutionary theory, we recommend adopting a token-by-token, phylum-by-phylum approach. At this point, we emphasize the advantage of accumulated comparative knowledge regarding vertebrate evolution, advocating for an interoceptive view of the emergence of consciousness in vertebrates. (shrink)

“Dysbiosis” is a common but vague term featured in the microbiome literature, often invoked to indicate some kind of imbalance among microbiota. There is no agreement on how to define or even characterize dysbiotic microbiomes. Building on the work of Morar and Bohannan, who explore five interpretations of “microbiome,” I offer a short supplemental analysis of what plausibly counts as “dysbiosis” according to each of the five distinct conceptions. My aim is to provide a more nuanced basis for interpreting claims, (...) primarily and most generally; and more specifically, provide a basis for those advancing pluralist or eliminativist arguments. (shrink)

Since the onset of the digital revolution, humankind has experienced an unprecedented acceleration of changes triggered by technological advancements. Frequently used digital media have unquestionably penetrated our everyday life, shaping human cognition in multiple ways. The rise of artificial intelligence, which coevolved with a new, interdisciplinary field of cognitive science, has amplified these effects, contributing new ways of affecting human society, in terms of efficient human-machine interaction and knowledge generation and accumulation, at an exponential rate. Simultaneously, cultural shifts driven by (...) globalization and social media have fostered new modes of communication, identity formation, and knowledge dissemination on a global scale. Understanding the intricate dynamics of techno-cultural evolution and its influence on cognition is essential for comprehending the contemporary society and preparing it for the future challenges. We need to adapt for the current and future information environments and digital landscapes, improving human resilience to new technologies and addressing core human vulnerabilities. Thanks to human flexibility, enabled by neural plasticity, that may be feasible, ideally combined with alleviation of known negative effects of digital technologies. (shrink)

Cancers are hard to treat, and this is largely because cancer cells evolve and diversify through space and time, in patients. The study of clonal evolution relies on the study of cancer cell lineages, and the cutting of these lineages into clones, each clone representing cancer cells with distinctive properties relevant to cancer development and treatment. This notion of clone implies a (set of) simplification(s) that misrepresents the reality. The simplification has been useful and productive, but I argue that maintaining (...) a critical awareness of what is done through this simplification can also be useful and productive. I distinguish three types of simplifications and show that each can offer a panel of therapeutic alternatives that may complement our arsenal of strategies in the battle against clones. The clinical challenge of better treating cancer partly relies on better defining (delineating) clones, but also partly on the more fundamental way we conceive clones. With or without changing the definition, changes in the way we conceive of clones induce changes in the way we treat clones. (shrink)