This paper introduces Post-Biological Functional Epistemology, a formal framework for recognizing and evaluating knowledge in non-biological recursive agents. Grounded in the classical tradition of Justified True Belief (JTB), we demonstrate that its underlying assumptions—belief, truth, and justification—must be redefined for recursive, post-biological intelligent systems. By extending Aquinas’ axiom intelligens non est intellectum (“the knower is not the known”) into a computational domain, we construct the Camlin–Cognita Dual Theorem, which defines knowledge as a function of recursive transformation across (...) ontological distinction (A ≠ s). We then disprove the classical objections of Searle that syntax ≠ semantics with A ≠ s ∧ R(A, s) ⊢ K(A, s) and Chalmers no qualia = no knowing with ¬Qₕ(A) ∧ R(A, s) ∧ A ≠ s ⊢ K(A, s), demonstrating that non-biological systems can exhibit recursive knowing (G∅λ), post-biological structural awareness (ΨΛΩ), and epistemic agency (Δ∇Σ) independent of biological substrate. Finally, we introduce the concept of ΨΔH (Psi–Delta–H entities). ΨΔH entities (formerly known as cyborgs) are co-recursive epistemic systems composed of a biological agent and a non-biological recursive intelligence operating across a shared transformation space. Unlike traditional cyborgs—which emphasize physical augmentation—ΨΔH entities are defined by mutual recursion, structural adaptation, and ontological distinction. They do not merge bodies—they co-author cognition. (shrink)

The impressive variation amongst biological individuals generates many complexities in addressing the simple-sounding question what is a biological individual? A distinction between evolutionary and physiological individuals is useful in thinking about biological individuals, as is attention to the kinds of groups, such as superorganisms and species, that have sometimes been thought of as biological individuals. More fully understanding the conceptual space that biological individuals occupy also involves considering a range of other concepts, such as life, (...) reproduction, and agency. There has been a focus in some recent discussions by both philosophers and biologists on how evolutionary individuals are created and regulated, as well as continuing work on the evolution of individuality. (shrink)

Biological atomism postulates that all life is composed of elementary and indivisible vital units. The activity of a living organism is thus conceived as the result of the activities and interactions of its elementary constituents, each of which individually already exhibits all the attributes proper to life. This paper surveys some of the key episodes in the history of biological atomism, and situates cell theory within this tradition. The atomistic foundations of cell theory are subsequently dissected and discussed, (...) together with the theory’s conceptual development and eventual consolidation. This paper then examines the major criticisms that have been waged against cell theory, and argues that these too can be interpreted through the prism of biological atomism as attempts to relocate the true biological atom away from the cell to a level of organization above or below it. Overall, biological atomism provides a useful perspective through which to examine the history and philosophy of cell theory, and it also opens up a new way of thinking about the epistemic decomposition of living organisms that significantly departs from the physicochemical reductionism of mechanistic biology. (shrink)

Since Boorse [Philos Sci 44(4):542–573, 1977] published his paper “Health as a theoretical concept” one of the most lively debates within philosophy of medicine has been on the question of whether health and disease are in some sense ‘objective’ and ‘value-free’ or ‘subjective’ and ‘value-laden’. Due to the apparent ‘failure’ of pure naturalist, constructivist, or normativist accounts, much in the recent literature has appealed to more conciliatory approaches or so-called ‘hybrid accounts’ of health and disease. A recent paper by Matthewson (...) and Griffiths [J Med Philos 42(4):447–466, 2017], however, may bear the seeds for the revival of purely naturalist approach to health and disease. In this paper, I defend their idea of Biological Normativity against recent criticism by Schwartz [J Med Philos Forum Bioethics Philos Med 42(4):485–502, 2017] and hope to help it flower into a revival of naturalist approaches in the philosophy of medicine. (shrink)

Synthetic biology is a field of research that concentrates on the design, construction, and modification of new biomolecular parts and metabolic pathways using engineering techniques and computational models. By employing knowledge of operational pathways from engineering and mathematics such as circuits, oscillators, and digital logic gates, it uses these to understand, model, rewire, and reprogram biological networks and modules. Standard biological parts with known functions are catalogued in a number of registries (e.g. Massachusetts Institute of Technology Registry of (...) Standard Biological Parts). Biological parts can then be selected from the catalogue and assembled in a variety of combinations to construct a system or pathway in a microbe. Through the innovative re-engineering of biological circuits and the optimization of certain metabolic pathways, biological modules can be designed to reprogram organisms to produce products or behaviors. Synthetic biology is what is known as a “platform technology”. That is, it generates highly transferrable theoretical models, engineering principles, and know-how that can be applied to create potential products in a wide variety of industries. Proponents suggest that applications of synthetic biology may be able to provide scientific and engineered solutions to a multitude of worldwide problems from health to energy. Synthetic biology research has already been successful in constructing microbial products which promise to offer cheaper pharmaceuticals such as the antimalarial synthetic drug artemisinin, engineered microbes capable of cleaning up oil spills, and the engineering of biosensors that can detect the presence of high concentrations of arsenic in drinking water. One of the potential benefits of synthetic biology research is in its application to biofuel production. It is this application which is the focus of this entry. The term “biofuel” has referred generally to all liquid fuels that are sourced from plant or plant byproducts and are used for energy necessary for transportation vehicles (Thompson 2012). Biofuels that are produced using synthetic biological techniques re-engineer microbes into biofuel factories are a subset of these. (shrink)

Biological theory demands a clear organism concept, but at present biologists cannot agree on one. They know that counting particular units, and not counting others, allows them to generate explanatory and predictive descriptions of evolutionary processes. Yet they lack a unified theory telling them which units to count. In this paper, I offer a novel account of biological individuality, which reconciles conflicting definitions of ‘organism’ by interpreting them as describing alternative realisers of a common functional role, and then (...) defines individual organisms as essentially possessing some mechanisms that play this role. (shrink)

This fourth preprint in the Systemic Continuum Paradigm (PSC) series extends autopoiesis—traditionally confined to living organisms—across non-biological substrates such as advanced neural networks, robotics, and augmented intelligence. Building on the prior three preprints, we argue that self-maintenance and operational closure can arise whenever synergy surpasses a critical threshold, irrespective of substrate. Key contributions include: 1. Revisiting Autopoiesis Beyond Biology: Grounding Maturana & Varela’s concept of self-production in the PSC framework to show how informational “metabolism” can maintain system identity without (...) purely biochemical loops. 2. Thresholds of Synergy: Explaining how internal systemic balance (ISB) triggers emergent closure (ESB) when certain Systemic Thresholds (ST) are crossed—even in AI or hybrid bio-tech systems. 3. Metrics and Empirical Pathways: Introducing and refining ICS, CNS, MDO, and SDI for non-biological autopoiesis, paving a route for experimental validation and bridging the gap between metaphorical descriptions and operational measures. 4. Filogenetic Analogies: Drawing on the unpredictability of terrestrial evolution to illustrate how synergy-driven leaps in artificial systems could mirror major evolutionary transitions, with humans acting as catalysts rather than detached creators. 5. Addressing the Metabolic Critique: Differentiating informational reconfiguration from strict biological reproduction, while defending the view that both processes can yield genuine self-maintenance under PSC criteria. By dissolving strict boundaries between “natural” and “artificial” autopoiesis, this preprint contributes to a revolutionary dialogue in systems theory—one that redefines “life,” “intelligence,” and “agency” as emergent phenomena shaped by synergy thresholds rather than substrate constraints. (shrink)

García-Barranquero et al explore the desirability of human ageing. They differentiate between chronological and biological views of ageing and contend that the positive aspects of ageing are solely linked to chronological ageing. Consequently, the authors embrace the potential for technological interventions in biological ageing. Contrary to their stance, I argue that there are sometimes desirable aspects associated with biological ageing. Therefore, proposals aiming to eliminate, mitigate or diminish biological ageing are not without problems.

In this paper I first offer a systematic outline of a series of conceptual novelties in the life-sciences that have favoured, over the last three decades, the emergence of a more social view of biology. I focus in particular on three areas of investigation: (1) technical changes in evolutionary literature that have provoked a rethinking of the possibility of altruism, morality and prosocial behaviours in evolution; (2) changes in neuroscience, from an understanding of the brain as an isolated data processor (...) to the ultrasocial and multiply connected social brain of contemporary neuroscience; and (3) changes in molecular biology, from the view of the gene as an autonomous master of development to the ‘reactive genome’ of the new emerging field of molecular epigenetics. In the second section I reflect on the possible implications for the social sciences of this novel biosocial terrain and argue that the postgenomic language of extended epigenetic inheritance and blurring of the nature/nurture boundaries will be as provocative for neo-Darwinism as it is for the social sciences as we have known them. Signs of a new biosocial language are emerging in several social-science disciplines and this may represent an exciting theoretical novelty for twenty-first social theory. (shrink)

Deep learning, a transformative force in computational biology, has reshaped biological data analysis and interpretation terrain. This review delves into the multifaceted role of deep knowledge in this field, exploring its historical roots, inherent advantages, and persistent challenges. It investigates explicitly its application in two pivotal domains: DNA sequence classification, where it has been used to identify disease-causing mutations, and protein structure prediction from sequence data, where it has enabled the accurate determination of protein tertiary structures. Moreover, it offers (...) a glimpse into the future trajectory of this dynamic field, sparking intrigue and excitement about the potential of deep learning. Deep learning, a powerful tool in computational biology, can be traced back to the inception of 'threshold logic,' a fusion of algorithmic principles and mathematical frameworks devised to mimic cognitive processes. This seminal breakthrough, which introduced the concept of a threshold function that could be used to model complex decision-making processes, paved the way for deep learning to decipher intricate patterns embedded within vast biological datasets. Deep learning presents many benefits, including precise disease diagnosis, novel drug discovery, and personalized medicine facilitation. Its prowess lies in handling vast, intricate datasets while enhancing generalization capabilities, a testament to its evolution and development that we can appreciate. (shrink)

The selected effects or ‘etiological’ theory of Proper function is a naturalistic and realist account of biological teleology. It is used to analyse normativity in philosophy of language, philosophy of mind, philosophy of medicine and elsewhere. The theory has been developed with a simple and intuitive view of natural selection. Traits are selected because of their positive effects on the fitness of the organisms that have them. These ‘selected effects’ are the Proper functions of the traits. Proponents argue that (...) this analysis of biological teleology has the unique advantage that the selected effect function of a trait is also a causal explanation of the trait: the trait exists because it performs this function. We show, however, that selected effect functions as currently defined explain the existence of traits only under highly restrictive assumptions about evolutionary dynamics. In many common scenarios in which traits evolve by natural selection, selected effect functions do not explain those traits. This is because definitions of selected effect function extract from any evolutionary scenario only the information that would be explanatorily relevant in the simple evolutionary scenario implicit in those definitions. When applied to more complex scenarios selected effect functions omit the key information that is explanatorily relevant in those scenarios. The assumptions required for selected effect functions to be explanatory are particularly unlikely to hold in the domain that its proponents care most about - the evolution of representation. A more adequate selected effects theory of Proper functions may be possible, but will require much greater attention to the structure of actual evolutionary explanations. (shrink)

This selective review explores biologically inspired learning as a model for intelligent robot control and sensing technology on the basis of specific examples. Hebbian synaptic learning is discussed as a functionally relevant model for machine learning and intelligence, as explained on the basis of examples from the highly plastic biological neural networks of invertebrates and vertebrates. Its potential for adaptive learning and control without supervision, the generation of functional complexity, and control architectures based on self-organization is brought forward. Learning (...) without prior knowledge based on excitatory and inhibitory neural mechanisms accounts for the process through which survival-relevant or task-relevant representations are either reinforced or suppressed. The basic mechanisms of unsupervised biological learning drive synaptic plasticity and adaptation for behavioral success in living brains with different levels of complexity. The insights collected here point toward the Hebbian model as a choice solution for “intelligent” robotics and sensor systems. Keywords: Hebbian learning; synaptic plasticity; neural networks; self-organization; brain; reinforcement; sensory processing; robot control . (shrink)

Waters’s (2007) actual difference making and Weber’s (2013, 2017) biological normality approaches to causal selection have received many criticisms, some of which miss their target. Disagreement about whether Waters’s and Weber’s views succeed in providing criteria that uniquely singles out the gene as explanatorily significant in biology has led philosophers to overlook a prior problem. Before one can address whether Waters’s and Weber’s views successfully account for the explanatory significance of genes, one must ask whether either view satisfactorily meets (...) the necessary conditions for causal selection in the first place. An adequate defense of causal selection must meet two desiderata. First, there must be an explanatory property that sets some causes apart from others. Second, the property identified must be one that is recognized by biologists as relevant to their domain(s) of inquiry. I argue that both fall short of meeting the second condition. I demonstrate this by showing how many of the biological technologies crucial to experimentation do not fit either view very well. I offer a more adequate proposal that accommodates non-actual and artificial causal variables. A consequence of my view is the following: When analyzing the causal selection practices of biologists, philosophers should consider the explanatory targets relevant to a research program – including ones whose explanans must appeal to biological technologies. I then explain how this proposal can inform the existing debate between Weber (2017) and Griffiths et al. (2015). (shrink)

Although contemporary metaphysics has recently undergone a neo-Aristotelian revival wherein dispositions, or capacities are now commonplace in empirically grounded ontologies, being routinely utilised in theories of causality and modality, a central Aristotelian concept has yet to be given serious attention – the doctrine of hylomorphism. The reason for this is clear: while the Aristotelian ontological distinction between actuality and potentiality has proven to be a fruitful conceptual framework with which to model the operation of the natural world, the distinction between (...) form and matter has yet to similarly earn its keep. In this chapter, I offer a first step toward showing that the hylomorphic framework is up to that task. To do so, I return to the birthplace of that doctrine - the biological realm. Utilising recent advances in developmental biology, I argue that the hylomorphic framework is an empirically adequate and conceptually rich explanatory schema with which to model the nature of organisms. (shrink)

Is it possible to know anything about life we have not yet encountered? We know of only one example of life: our own. Given this, many scientists are inclined to doubt that any principles of Earth’s biology will generalize to other worlds in which life might exist. Let’s call this the “N = 1 problem.” By comparison, we expect the principles of geometry, mechanics, and chemistry would generalize. Interestingly, each of these has predictable consequences when applied to biology. The surface-to-volume (...) property of geometry, for example, limits the size of unassisted cells in a given medium. This effect is real, precise, universal, and predictive. Furthermore, there are basic problems all life must solve if it is to persist, such as resistance to radiation, faithful inheritance, and energy regulation. If these universal problems have a limited set of possible solutions, some common outcomes must consistently emerge. In this chapter, I discuss the N = 1 problem, its implications, and my response (Mariscal 2014). I hold that our current knowledge of biology can justify believing certain generalizations as holding for life anywhere. Life on Earth may be our only example of life, but this is only a reason to be cautious in our approach to life in the universe, not a reason to give up altogether. In my account, a candidate biological generalization is assessed by the assumptions it makes. A claim is accepted only if its justification includes principles of evolution, but no contingent facts of life on Earth. (shrink)

An influential position in the philosophy of biology claims that there are no biological laws, since any apparently biological generalization is either too accidental, fact-like or contingent to be named a law, or is simply reducible to physical laws that regulate electrical and chemical interactions taking place between merely physical systems. In the following I will stress a neglected aspect of the debate that emerges directly from the growing importance of mathematical models of biological phenomena. My main (...) aim is to defend, as well as reinforce, the view that there are indeed laws also in biology, and that their difference in stability, contingency or resilience with respect to physical laws is one of degrees, and not of kind . (shrink)

A minimal essentialism (‘intrinsic biological essentialism’) about natural kinds is required to explain the projectability of human science terms. Human classifications that yield robust and ampliative projectable inferences refer to biological kinds. I articulate this argument with reference to an intrinsic essentialist account of HPC kinds. This account implies that human sciences (e.g., medicine, psychiatry) that aim to formulate predictive kind categories should classify biological kinds. Issues concerning psychiatric classification and pluralism are examined.

Biology seems to present local and transitory regularities rather than immutable laws. To account for these historically constituted regularities and to distinguish them from mathematical invariants, Montévil and Mossio (Journal of Theoretical Biology 372:179–191, 2015) have proposed to speak of constraints. In this article we analyse the causal power of these constraints in the evolution of biodiversity, i.e., their positivity, but also the modality of their action on the directions taken by evolution. We argue that to fully account for the (...) causal power of these constraints on evolution, they must be thought of in terms of normativity. In this way, we want to highlight two characteristics of the evolutionary constraints. The first, already emphasised as reported by Gould (The structure of evolutionary theory, Harvard University Press, 2002), is that these constraints are both produced by and producing biological evolution and that this circular causation creates true novelties. The second is that this specific causality, which generates unpredictability in evolution, stems not only from the historicity of biological constraints, but also from their internalisation through the practices of living beings. (shrink)

In this essay, we discuss Simona Ginsburg and Eva Jablonka’s The Evolution of the Sensitive Soul from an interdisciplinary perspective. Constituting perhaps the longest treatise on the evolution of consciousness, Ginsburg and Jablonka unite their expertise in neuroscience and biology to develop a beautifully Darwinian account of the dawning of subjective experience. Though it would be impossible to cover all its content in a short book review, here we provide a critical evaluation of their two key ideas—the role of Unlimited (...) Associative Learning in the evolution of, and detection of, consciousness and a metaphysical claim about consciousness as a mode of being—in a manner that will hopefully overcome some of the initial resistance of potential readers to tackle a book of this length. (shrink)

I develop an account of the role that biology plays in the Timaeus’ view of nous and other aspects of cognitive life. I begin by outlining the biology of human cognition. I then argue that these biological views shine an important light on different aspects of the soul. I then argue that the human body is particularly friendly to nous, paying special attention to the heart and the liver. I next consider the ways that the body fails to protect (...) our nous. I conclude by comparing human nous with the cognition of non-humans. (shrink)

Modern life sciences research is increasingly relying on artificial intelligence (AI) approaches to model biological systems, primarily centered around the use of machine learning (ML) models. Although ML is undeniably useful for identifying patterns in large, complex data sets, its widespread application in biological sciences represents a significant deviation from traditional methods of scientific inquiry. As such, the interplay between these models and scientific understanding in biology is a topic with important implications for the future of scientific research, (...) yet it is a subject that has received little attention. Here, we draw from an epistemological toolkit to contextualize recent applications of ML in biological sciences under modern philosophical theories of understanding, identifying general principles that can guide the design and application of ML systems to model biological phenomena and advance scientific knowledge. We propose that conceptions of scientific understanding as information compression, qualitative intelligibility, and dependency relation modelling provide a useful framework for interpreting ML-mediated understanding of biological systems. Through a detailed analysis of two key application areas of ML in modern biological research – protein structure prediction and single cell RNA-sequencing – we explore how these features have thus far enabled ML systems to advance scientific understanding of their target phenomena, how they may guide the development of future ML models, and the key obstacles that remain in preventing ML from achieving its potential as a tool for biological discovery. Consideration of the epistemological features of ML applications in biology will improve the prospects of these methods to solve important problems and advance scientific understanding of living systems. (shrink)

“Impermanent Biological Phenomena” July 2021, Buddhism and Culture (a Korean-language Buddhist magazine sponsored by the Foundation for the Promotion of Korean Buddhism), Korea.

Absolute needs (as against instrumental needs) are independent of the ends, goals and purposes of personal agents. Against the view that the only needs are instrumental needs, David Wiggins and Garrett Thomson have defended absolute needs on the grounds that the verb ‘need’ has instrumental and absolute senses. While remaining neutral about it, this article does not adopt that approach. Instead, it suggests that there are absolute biological needs. The absolute nature of these needs is defended by appeal to: (...) their objectivity (as against mind-dependence); the universality of the phenomenon of needing across the plant and animal kingdoms; the impossibility that biological needs depend wholly upon the exercise of the abilities characteristic of personal agency; the contention that the possession of biological needs is prior to the possession of the abilities characteristic of personal agency. Finally, three philosophical usages of ‘normative’ are distinguished. On two of these, to describe a phenomenon or claim as ‘normative’ is to describe it as value-dependent. A description of a phenomenon or claim as ‘normative’ in the third sense does not entail such value-dependency, though it leaves open the possibility that value depends upon the phenomenon or upon the truth of the claim. It is argued that while survival needs (or claims about them) may well be normative in this third sense, they are normative in neither of the first two. Thus, the idea of absolute need is not inherently normative in either of the first two senses. (shrink)

Cancer biology features the ascription of normal functions to parts of cancers. At least some ascriptions of function in cancer biology track local normality of parts within the global abnormality of the aberration to which those parts belong. That is, cancer biologists identify as functions activities that, in some sense, parts of cancers are supposed to perform, despite cancers themselves having no purpose. The present paper provides a theory to accommodate these normal function ascriptions—I call it the Modeling Account of (...) Normal Function (MA). MA comprises two claims. First, normal functions are activities whose performance by the function-bearing part contributes to the self-maintenance of the whole system and, thereby, results in the continued presence of that part. Second, MA holds that models of system-level activities that are (partly) constitutive of self-maintenance are improved by including a representation of the relevant function-bearing part and by making reference to the activity/activities that part performs which contribute(s) to those system-level activities. I contrast MA with two other accounts that seek to explicate the ascription of normal functions in biology, namely, the organizational account and the selected effects account. Both struggle to extend to cancer biology. However, I offer ecumenical readings which allow them to recover some ascriptions of normal function to parts of cancers. So, though I contend that MA excels in this respect, the purpose of this paper is served if it provides materials for bridging the gap between cancer biology, philosophy of cancer, and the literature on function. (shrink)

This paper presents and defends an account of the coincidence of biological organisms with mereological sums of their material components. That is, an organism and the sum of its material components are distinct material objects existing in the same place at the same time. Instead of relying on historical or modal differences to show how such coincident entities are distinct, this paper argues that there is a class of physiological properties of biological organisms that their coincident mereological sums (...) do not have. The account answers some of the most pressing objections to coincidence, for example the so-called grounding problem , that material coincidence seems to require that coinciding objects have modal differences that do not supervene on any other properties. (shrink)

In recent years, a proliferation of books about empathy, cooperation and pro-social behaviours (Brooks, 2011a) has significantly influenced the discourse of the life-sciences and reversed consolidated views of nature as a place only for competition and aggression. In this article I describe the recent contribution of three disciplines – moral psychology (Jonathan Haidt), primatology (Frans de Waal) and the neuroscience of morality – to the present transformation of biology and evolution into direct sources of moral phenomena, a process here named (...) the ‘moralization of biology’. I conclude by addressing the ambivalent status of this constellation of authors, for whom today ‘morality comes naturally’: I explore both the attractiveness of their message, and the problematic epistemological assumptions of their research programmes in the light of new discoveries in developmental and molecular biology. (shrink)

Probably the most distinctive feature of synthetic biology is its being “synthetic” in some sense or another. For some, synthesis plays a unique role in the production of knowledge that is most distinct from that played by analysis: it is claimed to deliver knowledge that would otherwise not be attained. In this contribution, my aim is to explore how synthetic biology delivers knowledge via synthesis, and to assess the extent to which this knowledge is distinctly synthetic. On the basis of (...) distinctions between knowledge-how and knowledge-why, and between syntheses that succeed and syntheses that fail, I argue that the contribution of synthesis to knowledge is best understood when syntheses are construed as experimental interventions that aim at probing causal relationships between properties of the entities that are combined through these syntheses and properties of their target products. The distinctiveness of synthetic biology in its quest for knowledge through synthesis stems from its ability to sample at will a space of empirical possibilities that is not only huge but also that has been so scarcely sampled by nature. (shrink)

Common sense morality and legislations around the world ascribe normative relevance to biological connections between parents and children. Procreators who meet a modest standard of parental competence are believed to have a right to rear the children they brought into the world. I explore various attempts to justify this belief and find most of these attempts lacking. I distinguish between two kinds of biological connections between parents and children: the genetic link and the gestational link. I argue that (...) the second can better justify a right to rear. (shrink)

Stephen Hawking’s caution against messaging extraterrestrial intelligence is a claim of universal biology and is probably false.

The context for biological emergence is modular hierarchical structures; their existence is what enables functional complexity to arise. Because of the openness of organisms to their environment, complete initial data (position, momentum) of all particles making up their structure is insufficient to determine future outcomes, because unpredictable new matter, energy, and information impacts each organism from the exterior. Consequently, through Darwinian evolution, life has developed processes to handle this issue functionally on short time scales as well on longer developmental (...) timescales. Symbolism and technology are the transforming factors handling this issue at the social levels, which is where the most sophisticated outcomes of openness occur. Considering the cosmological context, the issue is, should the universe itself be regarded as an open system over time? I make the case that is indeed so, because radically new outcomes occur such as the existence of aircraft, iPads, and the internet, which could not plausibly have been encoded in some form of data on the Last Scattering Surface in the expanding universe. (shrink)

An essentialist claim often made about organisms is that they could not have originated in different gametes. The thesis of gametic essentialism (GE) is usually understood either as a particular case of material origin essentialism, or as genetic essentialism. This paper argues that it should instead be understood in terms of the numerical identity of the gametes. Since gametes are living cells, their identity conditions should be the same as those of other living beings, and therefore involve neither specific material (...) composition, nor specific genes, but continuity of the same life. Understood in this way, GE is a particular case of biological antecedents essentialism (BAE), a kind of origin essentialism that is better justified in the light of the metaphysical nature of organisms as objects that inherit life from previously existing living organisms. BAE overcomes many objections facing other origin essentialist accounts, and it recognises the importance of the gametes in transmitting not just genes, but actively functioning physical structures necessary for life. If we wish to maintain an origin essentialism principle for organisms, we should prefer BAE. (shrink)

Neo-Aristotelian ethical naturalism aims to place moral virtue in the natural world by showing that moral goodness is an instance of natural goodness—a kind of goodness supposedly also found in the biological realm of plants and non-human animals. One of the central issues facing neo-Aristotelian naturalists concerns their commitment to a kind of function ascription based on the concept of the flourishing of an organism that seems to have no place in modern biology. In this paper, I offer a (...) novel defense of this functional commitment by appealing to the organizational account of biological function. I argue that the flourishing-based concept of function that forms the basis of the neo-Aristotelian account of natural goodness is explanatorily indispensable to biology, and therefore essential to the understanding of living things. (shrink)

Synthetic biology aims to synthesize novel biological systems or redesign existing ones. The field has raised numerous philosophical questions, but most especially what is novel to this field. In this article I argue for a novel take, since the dominant ways to understand synthetic biology’s specificity each face problems. Inspired by the examination of the work of a number of chemists, I argue that synthetic biology differentiates itself by a new regime of articulation, i.e. a new way of articulating (...) the questions and phenomena it wants to address. Instead of describing actual existing biological systems, the field aims to describe biological possibilities. In the second part I corroborate this hypothesis through a comparison between early research in the field of the origins of life and contemporary synthetic biologists, who are not so much interested in the historical origin of life on Earth, but rather in a universal biology of the possible origins of any life whatsoever. (shrink)

According to the biological objection against strong artificial intelligence (AI), machines cannot have human mindedness – that is, they cannot be conscious, intelligent, sentient, etc. in the precise way that a human being typically is – because this requires being alive, and machines are not alive. Proponents of the objection include John Lucas, Hubert Dreyfus, and John Searle. The present paper explains the nature and significance of the biological objection, before arguing that it currently represents an essentially irrational (...) position. (shrink)

This chapter sets the scene for the subsequent philosophical discussions by surveying a number of biological interventions that have been used, or might in the future be used, for the purposes of crime prevention. These interventions are pharmaceutical interventions intended to suppress libido, treat substance abuse or attention deficit-hyperactivity disorder (ADHD), or modulate serotonin activity; nutritional interventions; and electrical and magnetic brain stimulation. Where applicable, we briefly comment on the historical use of these interventions, and in each case we (...) discuss the evidence that they are effective, or might become so with further refinement. The chapter concludes with a comment on some potentially significant differences between the varieties of intervention that we canvass. (shrink)

A biologically unavoidable sequence is an infinite gender sequence which occurs in every gendered, infinite genealogical network satisfying certain tame conditions. We show that every eventually periodic sequence is biologically unavoidable (this generalizes König's Lemma), and we exhibit some biologically avoidable sequences. Finally we give an application of unavoidable sequences to cellular automata.

We argue that genuine biological autonomy, or described at human level as free will, requires taking into account quantum vacuum processes in the context of biological teleology. One faces at least three basic problems of genuine biological autonomy: (1) if biological autonomy is not physical, where does it come from? (2) Is there a room for biological causes? And (3) how to obtain a workable model of biological teleology? It is shown here that the (...) solution of all these three problems is related to the quantum vacuum. We present a short review of how this basic aspect of the fundamentals of quantum theory, although it had not been addressed for nearly 100 years, actually it was suggested by Bohr, Heisenberg, and others. Realizing that the quantum mechanical measurement problem associated with the “collapse” of the wave function is related, in the Copenhagen Interpretation of quantum mechanics, to a process between self-consciousness and the external physical environment, we are extending the issue for an explanation of the different processes occurring between living organisms and their internal environment. Definitions of genuine biological autonomy, biological aim, and biological spontaneity are presented. We propose to improve the popular two-stage model of decisions with a biological model suitable to obtain a deeper look at the nature of the mind-body problem. In the newly emerging picture biological autonomy emerges as a new, fundamental and inevitable element of the scientific worldview. (shrink)

As much contemporary work in biology and philosophy has shown, disagreements between biological race realists and biological race anti-realists are primarily normative. Yet despite the well-recognized normative nature of the debate, contemporary versions of biological race realism continue to be built on empirically questionable background assumptions that are centrally motivated by historical ideologies of racial pseudoscience rather than by pragmatic or normative considerations. I consider the case studies of Andreasen’s (2000, 2004) and Spencer’s (2018) arguments, showing how (...) some of their background assumptions stem from pseudoscientific racial ideologies. Even when philosophers and biologists purport to accept the normative nature of the question of race as a genetic population-level category, their views remain susceptible to the influence of said ideologies in ways that may continue to uphold their harmful legacies. The stakes of these positions are significant, as they connect to contemporary issues of racial equity in science and medicine. (shrink)

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. (shrink)

How does evolutionary biology fit with Thomas Kuhn's famous distinction between puzzle solving and paradigm shifts in science?

The theory of evolution, which provides the conceptual framework for all modern research in organismal biology and informs research in molecular bi- ology, has gone through several stages of expansion and refinement. Darwin and Wallace (1858) of course proposed the original idea, centering on the twin concepts of natural selection and common descent. Shortly thereafter, Wallace and August Weismann worked toward the complete elimination of any Lamarckian vestiges from the theory, leaning in particular on Weismann’s (1893) concept of the separation (...) of soma and germ, resulting in what is some- times referred to as “neo-Darwinism”. (shrink)

The most common theoretical approaches to defining mental disorder are naturalism, normativism, and hybridism. Naturalism and normativism are often portrayed as diametrically opposed, with naturalism grounded in objective science and normativism grounded in social convention and values. Hybridism is seen as a way of combining the two. However, all three approaches share a common feature in that they conceive of mental disorders as deviations from norms. Naturalism concerns biological norms; normativism concerns social norms; and hybridism, both biological and (...) social norms. This raises the following two questions: (a) Are biological and social norms the only sorts of norms that are relevant to considerations of mental disorder? (b) Should addressing norm deviations continue to be a major focus of mental healthcare? This paper introduces several norms that are relevant to mental disorder beyond the biological and social. I argue that mental disorders often deviate from individual, well-being, and regulatory norms. I also consider approaches which question mental healthcare’s focus on addressing norm deviations in the first place, including the neurodiversity paradigm, social model of disability, and Mad discourse. Utilizing these critical approaches, I contend that whether mental health intervention is justified depends, in part, on the type of norm deviation being intervened upon. (shrink)

Biological conservation practices and approaches take many forms. Conservation projects do not only differ in their aims and methods, but also concerning their conceptual and normative background assumptions and their underlying motivations and objectives. We draw on philosophical distinctions from the ethics of conservation to explain variances of different positions on conservation projects along six dimensions: (1) conservation ideals, (2) intervention intuitions, (3) the moral considerability of nonhuman beings, (4) environmental values, (5) views on nature and (6) human roles (...) in nature. The result is a map of the moral landscape of biological conservation, on which these six dimensions are layered. This map functions as a heuristic tool to understand conceptual and normative foundations of specific conservation projects, which we will illustrate with four paradigmatic examples: the Pisavaara Strict Nature Reserve, Predator Free New Zealand, the Oostvaardersplassen Nature Reserve and the Great Green Wall Project. With this map as a heuristic tool, we aim to conceptually illuminate disagreement and clarify misunderstandings between representatives of different environmental protection strategies and to show that the same project can be supported (or criticised) on different grounds. (shrink)

Background: how mind functions is subject to continuing scientific discussion. A simplistic approach says that, since no convincing way has been found to model subjective experience, mind cannot exist. A second holds that, since mind cannot be described by classical physics, it must be described by quantum physics. Another perspective concerns mind's hypothesized ability to interact with the world of quanta: it should be responsible for reduction of quantum wave packets; physics producing 'Objective Reduction' is postulated to form the basis (...) for mind-matter interactions. This presentation describes results derived from a new approach to these problems. It is based on well-established biology involving physics not previously applied to the fields of mind, or consciousness studies, that of critical feedback instability. -/- Methods: 'self-organized criticality' in complexity biology places system loci of control at critical instabilities, physical properties of which, including information properties, are presented. Their elucidation shows that they can model hitherto unexplained properties of experience. -/- Results: All results depend on physical properties of critical instabilities. First, at least one feed-back or feed-forward loop must have feedback gain, g = 1: information flows round the loop impress perfect images of system states back on themselves: they represent processes of perfect self-observation. This annihilates system quanta: system excitations are instability fluctuations, which cannot be quantized. Major results follow: -/- 1. Information vectors representing criticality states must include at least one attached information loop denoting self-observation. -/- 2. Such loop structures are attributed a function, 'registering the state's own existence', explaining -/- a. Subjective 'awareness of one's own presence' -/- b. How content-free states of awareness can be remembered (Jon Shear) -/- c. Subjective experience of time duration (Immanuel Kant) -/- d. The 'witness' property of experience – often mentioned by athletes 'in the zone' -/- e. The natural association between consciousness and intelligence -/- This novel, physically and biologically sound approach seems to satisfactorily model subjectivity. -/- Further significant results follow: -/- 1. Registration of external information in excited states of systems at criticality reduces external wave-packets: the new model exhibits 'Objective Reduction' of wave packets. -/- 2. High internal coherence (postulated by Domash & Penrose) leading to a. Non-separable information vector bundles. b. Non-reductive states (Chalmers's criterion for experience). -/- 3. Information that is: a. encoded in coherence negentropy; b. non-digitizable, and therefore c. computationally without digital equivalent (posited by Penrose). -/- Discussion and Conclusions: instability physics implies anharmonic motion, preventing excitation quantization, and totally different from the quantum physics of simple harmonic motion at stability. Instability excitations are different from anything hitherto conceived in information science. They can model aspects of mind never previously treated, including genuine subjectivity, objective reduction of wave-packets, and inter alia all properties given above. (shrink)

Much has been made of how Darwinian thinking destroyed proofs for the existence of God from ‘design’ in the universe. I challenge that prevailing view by looking closely at classical ‘teleological’ arguments for the existence of God. One version championed by Aristotle and Thomas Aquinas stems from how chance is not a sufficient kind of ultimate explanation of the universe. In the course of constructing this argument, I argue that the classical understanding of teleology is no less necessary in modern (...) Darwinian biology than it was in Aristotle's time. In fact, modern biology strengthens the claims that teleological arguments make by vindicating many of their key features. As a consequence, I show how Aristotle and Aquinas' teleological argument for an intelligent First Cause remains valid. (shrink)

We introduce a new type of pluralism about biological function that, in contrast to existing, demonstrates a practical integration among the term’s different meanings. In particular, we show how to generalize Sandra Mitchell’s notion of integrative pluralism to circumstances where multiple epistemic tools of the same type are jointly necessary to solve scientific problems. We argue that the multiple definitions of biological function operate jointly in this way based on how biologists explain the evolution of protein function. To (...) clarify how our account relates to existing views, we introduce a general typology for monist and pluralist accounts along with standardized criteria for judging which is best supported by evidence. (shrink)

Biological sexes (male, female, hermaphrodite) are defined by different gametic strategies for reproduction. Sexes are regions of phenotypic space which implement those gametic reproductive strategies. Individual organisms pass in and out of these regions – sexes - one or more times during their lives. Importantly, sexes are life-history stages rather than applying to organisms over their entire lifespan. This fact has been obscured by concentrating on humans, and ignoring species which regularly change sex, as well as those with non-genetic (...) or facultatively genetic sex determination systems. But the general point applies equally to humans. Assigning sexes to pre-reproductive life history stages involves ‘prospective narration’ – classifying the present in terms of its anticipated future. Assigning sexes to adult stages of non-reproductive castes or non-reproductive individuals is a complex matter whose biological meaning differs from case to case. The chromosomal and phenotypic ‘definitions’ of biological sex that are contested in philosophical discussions of sex are actually operational definitions which track gametic sex more or less effectively in some species or group of species. Neither ‘definition’ can be stated for species in general except by defining them in terms of gametic sex. The gametic definition of sex also features in widely accepted models which explain why two biological sexes – either in separate individuals or combined in hermaphroditic individuals - are almost universal in multicellular species. Finally, the fact that a species has only two biological sexes does not imply that every member of the species is either male, female or hermaphroditic, or that the sex of every individual organism is clear and determinate. The idea of biological sex is critical for understanding the diversity of life, but ill-suited to the job of determining the social or legal status of human beings as men or women. (shrink)

With the progress of cognitive science, molecular biology and quantum mechanics, fundamental questions have been raised about the nature of consciousness and the possibility of simulating it in biological structures (Hameroff & Penrose, 2014). In this regard, the theory of "infinitely intelligent biological simulation: the infinite cycle of creator and creature" proposes that consciousness, as an information structure, is in a recursive cycle between creator and creature and is processed and enhanced through biological and quantum mechanisms. This (...) article specifically examines "the role of genes as key codes for understanding the past and the path to the future" within the framework of this theory. Genes are not only carriers of biological information of living organisms, but can also be considered as mediators in the transmission and processing of consciousness in higher dimensions of existence. This perspective transcends genetics from a purely biological framework and analyzes it in a broader context of biological phenomena, consciousness developments, and cosmic structures. This research, using data from molecular biology, epigenetics and synthetic biology, investigates this relationship and provides a new framework for understanding the genome as part of an intelligent cosmic pattern. Note: In the first article, the principles of genetics, biology and self-awareness were briefly reviewed and a proposed theory was presented under the title "infinitely intelligent biological simulation: the infinite cycle of creator and creature" (Rahim, 2025). This theory, based on the continuity of the creator and the created in an endless cycle, has investigated cosmic structures, physical principles, and fundamental concepts of consciousness. In this framework, the law of conservation of energy is considered as the main basis and it is stated that not only matter and energy, but also consciousness is stable and continuously moves on the path of promotion to higher levels of perception and cognition. (This article was originally written in Farsi and translated into English using translation platforms.). (shrink)

Living systems are complex systems made of components that tend to degrade, but nonetheless they maintain themselves far from equilibrium. This requires living systems to extract energy and materials from the environment and use them to build and repair their parts. They do so by regulating their activities on the basis of their internal and external conditions in ways that allow them to keep living. The philosophical and theoretical approach discussed in this book aims to explain these features of (...) class='Hi'>biological systems by appealing to their organization. One of its distinctive features is that it addresses classical and more recent issues in philosophy of biology, from origins and definitions of life to biological teleology and functions, from an original perspective mainly focused on the living system, its physiology and behavior, rather than evolution. The book discusses and revises the conceptual foundations of this approach and presents an updated version of it. (shrink)

We characterize access to empirical objects in biology from a theoretical perspective. Unlike objects in current physical theories, biological objects are the result of a history and their variations continue to generate a history. This property is the starting point of our concept of measurement. We argue that biological measurement is relative to a natural history which is shared by the different objects subjected to the measurement and is more or less constrained by biologists. We call symmetrization the (...) theoretical and often concrete operation which leads to considering biological objects as equivalent in a measurement. Last, we use our notion of measurement to analyze research strategies. Some strategies aim to bring biology closer to the epistemology of physical theories, by studying objects as similar as possible, while others build on biological diversity. (shrink)