Our understanding of the universe has grown rapidly in recent decades. We’ve discovered evidence of water in nearby planets, discovered planets outside our solar system, mapped the genomes of thousands of organisms, and probed the very origins and limits of life. The scientific perspective of life-as-it-could-be has expanded in part by research in astrobiology, synthetic biology, and artificial life. In the face of such scientific developments, we argue there is an ever-growing need for universal biology, life-as-it-must-be, the multidisciplinary study of (...) non-contingent aspects of life as guided by biological theory and constrained by the universe. We present three distinct but connected ways of universalizing biology—with respect to characterizing aspects of life everywhere, with respect to the explanatory scope of biological theory, and with respect to extending biological insights to the structure of nonbiological entities. For each of these, we sketch the theoretical goals and challenges, as well as give examples of current research that might be labeled universal biology. (shrink)

Despite numerous and increasing attempts to define what life is, there is no consensus on necessary and sufficient conditions for life. Accordingly, some scholars have questioned the value of definitions of life and encouraged scientists and philosophers alike to discard the project. As an alternative to this pessimistic conclusion, we argue that critically rethinking the nature and uses of definitions can provide new insights into the epistemic roles of definitions of life for different research practices. This paper examines the possible (...) contributions of definitions of life in scientific domains where such definitions are used most (e.g., Synthetic Biology, Origins of Life, Alife, and Astrobiology). Rather than as classificatory tools for demarcation of natural kinds, we highlight the pragmatic utility of what we call operational definitions that serve as theoretical and epistemic tools in scientific practice. In particular, we examine contexts where definitions integrate criteria for life into theoretical models that involve or enable observable operations. We show how these definitions of life play important roles in influencing research agendas and evaluating results, and we argue that to discard the project of defining life is neither sufficiently motivated, nor possible without dismissing important theoretical and practical research. (shrink)

This paper examines three exemplary theories of living organization with respect to their common feature of defining life in terms of metabolic closure: autopoiesis, (M, R) systems, and chemoton theory. Metabolic closure is broadly understood to denote the property of organized chemical systems that each component necessary for the maintenance of the system is produced from within the system itself, except for an input of energy. It is argued that two of the theories considered—autopoiesis and (M, R) systems—participate in a (...) hylomorphist pattern of thinking which separates the “form” of the living system from its “matter.” The analysis and critique of hylomorphism found in the work of the philosopher Gilbert Simondon is then applied to these two theories, and on the basis of this critique it is argued that the chemoton model offers a superior theory of minimal life which overcomes many of the problems associated with the other two. Throughout, the relationship between hylomorphism and the understanding of living things as machines is explored. The paper concludes by considering how hylomorphism as a background ontology for theories of life fundamentally influences the way life is defined. (shrink)

Uncontainable Life: A Biophilosophy of Bioart investigates the ways in which thinking through the contemporary hybrid artistico-scientific practices of bioart is a biophilosophical practice, one that contributes to a more nuanced understanding of life than we encounter in mainstream academic discourse. When examined from a Deleuzian feminist perspective and in dialogue with contemporary bioscience, bioartistic projects reveal the inadequacy of asking about life’s essence. They expose the enmeshment between the living and non-living, organic and inorganic, and, ultimately, life and death. (...) Instead of examining the defining criteria of life, bioartistic practices explore and enact life as processual, differential, and always already uncontainable, thus transcending preconceived material and conceptual boundaries. In this way, this doctoral thesis concentrates on the ontology of life as it emerges through the selected bioartworks: “semi-living” sculptures created by The Tissue Culture and Art Project and the performance May the Horse Live in Me by L’Art Orienté Objet. The hope is that such an ontology can enable future conceptualisations of an ethico-politics that avoids the anthropocentric logic dominant in the humanities and social sciences. (shrink)

Paper type: Conceptual perspective. Background(s): Physics, biology, epistemology Perspectives: Theory of autopoietic systems, Popperian evolutionary epistemology and the biology of cognition. Context: This paper is a contribution to developing the theories of hierarchically complex living systems and the natures of knowledge in such systems. Problem: Dissonance between the literatures of knowledge management and organization theory and my observations of the living organization led to consideration of foundation questions: What does it mean to be alive? What is knowledge? How are life (...) and knowledge related? Method: The approach is synthetic and multidisciplinary. The concept of autopoiesis (as defined by Maturana) as a definition for life, and knowledge as a product of autopoiesis are developed from first principles regarding the behavior of dynamical systems in time. Results: Autopoiesis and the construction of knowledge are inseparable aspects of physical phenomena scalable to many levels of organization (e.g., cells, multicellular organisms, organizations, social systems, etc.). The result unifies theories of epistemology, physical dynamics, life, biological evolution, knowledge and social systems. Implications: Results highlight the importance to understand autopoiesis as first defined by Maturana and Varela – as a complex physical phenomenon persisting over time. Autopoietic “self-observation” is not paradoxical. As dynamic physical processes, any internal/external activities relating to “observations” are displaced in time. The worlds living systems act on are not those observed. “Circularly closed” systems are actually open spirals along the axis of time. (shrink)

All of the attempts to date to find a set of necessary and sufficient conditions for life, in order to provide an essential definition of life, have failed. We only have at our disposal series of lists that contain diverse characteristics usually found in living beings. Some authors have drawn from this fact the conclusion that life is not a natural kind. It will be argued here that this conclusion is too hasty and that if life is understood as a (...) natural kind in the non-essentialist sense of a homeostatic property cluster, it is easy to see why the attempts to find a unique and essentialist definition of life have failed. Understanding life in this way would imply that the pretension to find such a type of definition should be abandoned. (shrink)

Is one of the roles of theory in biology answering the question “What is life?” This is true of theory in many other fields of science. So why should not it be the case for biology? Yet efforts to identify unifying concepts and principles of life have been disappointing, leading some (pluralists) to conclude that life is not a natural kind. In this essay I argue that such judgments are premature. Life as we know it on Earth today represents a (...) single example and moreover there is positive evidence that it may be unrepresentative of life considered generally. Furthermore, as I discuss, the prototype for theorizing about life has traditionally been based on multicellular plants and animals. Yet biologists have discovered that the latter represent a rare, exotic, and fairly recent form of Earth life. By far the oldest, toughest, most extensive, and diverse form of life on our planet is unicellular, prokaryotic microbes, and there are reasons to suppose that this is almost certainly true elsewhere in the universe as well. If there are explanatorily and predictively powerful, biologically distinctive principles for life that can be gleaned from our insular example of life it is more likely that they will be found among the microbes. I discuss some provocative ways in which unicellular microbes differ from multicellular eukaryotes and argue that some of them just might provide us with key insights into the nature of life. (shrink)

A number of areas of biology raise questions about what is of value in the natural environment and how we ought to behave towards it: conservation biology, environmental science, and ecology, to name a few. Based on my experience teaching students from these and similar majors, I argue that the field of environmental ethics has much to teach these students. They come to me with pent-up questions and a feeling that more is needed to fully engage in their subjects, and (...) I believe some exposure to environmental ethics can help focus their interests and goals. I identify three primary areas in which environmental ethics can con- tribute to their education. The first is an examination of who (or what) should be considered to be part of our moral community (i.e., the community to whom we owe direct duties). Is it humans only? Or does it include all sentient life? Or all life? Or ecosystems considered holistically? Often, readings implicitly assume one or more of these answers; the goal is to make the student more sensitive to these implicit claims and to get them to think about the different reasons that support them. The second area, related to the first, is the application of the different answers concerning the extent of the ethical community to real environmental issues and problems. Students need to be aware of how the different answers concerning the moral community can imply conflicting answers for how we should act in certain cases and to think about ways to move toward conflict resolution. The third area in which environmental ethics can contribute is a more conceptual one, focusing on central concepts such as biodiversity, sustainability, species, and ecosystems. Exploring and evaluating various meanings of these terms will make students more reflective and thoughtful citizens and biologists, sensitive to the implications that different conceptual choices make. (shrink)

Science is now studying biodiversity on a massive scale. These studies are occurring not just at the scale of larger plants and animals, but also at the scale of minute entities such as bacteria and viruses. This expansion has led to the development of a specific sub-field of “microbial diversity”. In this paper, I investigate how microbial diversity faces two of the classical issues encountered by the concept of “ biodiversity ”: the issues of defining the units of biodiversity and (...) of choosing a mathematical measure of diversity. I also show that the extension of the scope of biodiversity to microbial entities such as viruses and many other not-clearly-alive entities raises yet another foundational issue: that of defining a “lower-limit” of biodiversity. (shrink)

The question ‘what is life?’ has long been a source of philosophical debate and in recent years has taken on increasing scientific importance. The most popular approach among both philosophers and scientists for answering this question is to provide a “definition” of life. In this article I explore a variety of different definitional approaches, both traditional and non-traditional, that have been used to “define” life. I argue that all of them are deeply flawed. It is my contention that a scientifically (...) compelling understanding of the nature of life presupposes an empirically adequate scientific theory (vs. definition) of life; as I argue, scientific theories are not the sort of thing that can be encapsulated in definitions. Unfortunately, as I also discuss, scientists are currently in no position to formulate even a tentative version of such a theory. Recent discoveries in biology and biochemistry have revealed that familiar Earth life represents a single example that may not be representative of life. If this is the case, life on Earth today provides an empirically inadequate foundation for theorizing about life considered generally. I sketch a strategy for procuring the needed additional examples of life without the guidance of a definition or theory of life, and close with an application to NASA’s fledgling search for extraterrestrial life. (shrink)

What is the definition of life? Artificial life environments provide an interesting test case for this classical question. Understanding what such systems can tell us about biological life requires negotiating the tricky conceptual boundary between virtual and real life forms. Drawing from Wittgenstein’s analysis of the concept of a game and a Darwinian insight about classification, I argue that classifying life involves both causal and pragmatic elements. Rather than searching for a single, sharp definition, these considerations suggest that life is (...) a cluster concept with fuzzy boundaries and that there are multiple legitimate ways to make the notion precise for different scientific purposes. This pluralist, realist account avoids unnecessary border disputes by emphasizing how science negotiates such questions in relation to theory and evidence. I also discuss several objections to this approach, including a “moral hesitation” some have to allowing broader application of the concept of life to include artificial life. (shrink)

Our aim in the present paper is to approach the nature of life from the perspective of autonomy, showing that this perspective can be helpful for overcoming the traditional Cartesian gap between the physical and cognitive domains. We first argue that, although the phenomenon of life manifests itself as highly complex and multidimensional, requiring various levels of description, individual organisms constitute the core of this multifarious phenomenology. Thereafter, our discussion focuses on the nature of the organization of individual living entities, (...) proposing autonomy as the main concept to grasp it. In the second part of the article we show how autonomy is also fundamental to explaining major evolutionary transitions, in an attempt to rethink evolution from the point of view of the organizational structure of the entities/organisms involved. This gives further support to the idea of autonomy not only as a key to understanding life in general but also the complex expressions of it that we observe on our planet. Finally, we suggest a possible general principle that underlies those evolutionary transitions, which allow for the open-ended redefinition of autonomous systems: namely, the relative dynamic decoupling that must be articulated among distinct parts, modules or modes of operation in these systems. (shrink)

Darwin’s classic ‘Origin of Species’ (Darwin 1859) described forces of selection acting upon individuals, but there remains a great deal of controversy about what exactly the status and definition of a biological individual is. Recently some authors have argued that the individual is dispensable – that an inability to pin it down is not problematic because little rests on it anyway. The aim of this paper is to show that there is a real problem of biological individuality, and an urgent (...) need to arbitrate over the current plethora of solutions to it. (shrink)

The assumption that all life on Earth today shares the same basic molecular architecture and biochemistry is part of the paradigm of modern biology. This paper argues that there is little theoretical or empirical support for this widely held assumption. Scientists know that life could have been at least modestly different at the molecular level and it is clear that alternative molecular building blocks for life were available on the early Earth. If the emergence of life is, like other natural (...) phenomena, highly probable given the right chemical and physical conditions then it seems likely that the early Earth hosted multiple origins of life, some of which produced chemical variations on life as we know it. While these points are often conceded, it is nevertheless maintained that any primitive alternatives to familiar life would have been eliminated long ago, either amalgamated into a single form of life through lateral gene transfer (LGT) or alternatively out-competed by our putatively more evolutionarily robust form of life. Besides, the argument continues, if such life forms still existed, we surely would have encountered telling signs of them by now. These arguments do not hold up well under close scrutiny. They reflect a host of assumptions that are grounded in our experience with large multicellular organisms and, most importantly, do not apply to microbial forms of life, which cannot be easily studied without the aid of sophisticated technologies. Significantly, the most powerful molecular biology techniques available—polymerase chain reaction (PCR) amplification of rRNA genes augmented by metagenomic analysis—could not detect such microbes if they existed. Given the profound philosophical and scientific importance that such a discovery would represent, a dedicated search for ‘shadow microbes’ (heretofore unrecognized ‘alien’ forms of terran microbial life) seems in order. The best place to start such a search is with puzzling (anomalous) phenomena, such as desert varnish, that resist classification as ‘biological’ or ‘nonbiological’. Ó 2007 Elsevier Ltd.. (shrink)

The plurality of definitions of life is often perceived as an unsatisfying situation stemming from still incomplete knowledge about ‘what it is to live’ as well as from the existence of a variety of methods for reaching a definition. For many, such plurality is to be remedied and the search for a unique and fully satisfactory definition of life pursued. In this contribution on the contrary, it is argued that the existence of such a variety of definitions of life undermines (...) the very feasibility of ever reaching a unique unambiguous definition. It is argued that focusing on the definitions of specific types of ‘living systems’ – somehow in the same way that one can define specific types of ‘flying systems’ – could be more fruitful from a heuristic point of view than looking for ‘the’ right definition of life, and probably more accurate in terms of carving Nature at its joints. (shrink)

Despite hundreds of definitions, no consensus exists on a definition of life or on the closely related and problematic definitions of the organism and death. These problems retard practical and theoretical development in, for example, exobiology, artificial life, biology and evolution. This paper suggests improving this situation by basing definitions on a theory of a generalized particle hierarchy. This theory uses the common denominator of the “operator” for a unified ranking of both particles and organisms, from elementary particles to animals (...) with brains. Accordingly, this ranking is called “the operator hierarchy”. This hierarchy allows life to be defined as: matter with the configuration of an operator, and that possesses a complexity equal to, or even higher than the cellular operator. Living is then synonymous with the dynamics of such operators and the word organism refers to a select group of operators that fit the definition of life. The minimum condition defining an organism is its existence as an operator, construction thus being more essential than metabolism, growth or reproduction. In the operator hierarchy, every organism is associated with a specific closure, for example, the nucleus in eukaryotes. This allows death to be defined as: the state in which an organism has lost its closure following irreversible deterioration of its organization. The generality of the operator hierarchy also offers a context to discuss “life as we do not know it”. The paper ends with testing the definition’s practical value with a range of examples. (shrink)

In several disciplines within science—evolutionary biology, molecular biology, astrobiology, synthetic biology, artificial life—and outside science—primarily ethics—efforts to define life have recently multiplied. However, no consensus has emerged. In this article, I argue that this is no accident. I propose a dilemma showing that the project of defining life is either impossible or pointless. The notion of life at stake in this project is either the folk concept of life or a scientific concept. In the former case, empirical evidence shows that (...) life cannot be defined. In the latter case, I argue that, although defining life may be possible, it is pointless. I conclude that scientists, philosophers, and ethicists should discard the project of defining life. (shrink)

The assumption that all life on Earth today shares the same basic molecular architecture and biochemistry is part of the paradigm of modern biology. This paper argues that there is little theoretical or empirical support for this widely held assumption. Scientists know that life could have been at least modestly different at the molecular level and it is clear that alternative molecular building blocks for life were available on the early Earth. If the emergence of life is, like other natural (...) phenomena, highly probable given the right chemical and physical conditions then it seems likely that the early Earth hosted multiple origins of life, some of which produced chemical variations on life as we know it. While these points are often conceded, it is nevertheless maintained that any primitive alternatives to familiar life would have been eliminated long ago, either amalgamated into a single form of life through lateral gene transfer or alternatively out-competed by our putatively more evolutionarily robust form of life. Besides, the argument continues, if such life forms still existed, we surely would have encountered telling signs of them by now. These arguments do not hold up well under close scrutiny. They reflect a host of assumptions that are grounded in our experience with large multicellular organisms and, most importantly, do not apply to microbial forms of life, which cannot be easily studied without the aid of sophisticated technologies. Significantly, the most powerful molecular biology techniques available—polymerase chain reaction amplification of rRNA genes augmented by metagenomic analysis—could not detect such microbes if they existed. Given the profound philosophical and scientific importance that such a discovery would represent, a dedicated search for ‘shadow microbes’ seems in order. The best place to start such a search is with puzzling phenomena, such as desert varnish, that resist classification as ‘biological’ or ‘nonbiological’. (shrink)

According to the mainstream position in the bioethical definition of death debate, death is to be equated with the cessation of an organism. Given such a perspective, some bioethicists uphold the position that brain-dead patients are dead, while others claim that they are alive. Regardless of the specific opinion on the status of brain-dead patients, the mere bioethical concept of death, according to many bioethicists, has the merit of being unanimous and univocal, as well as grounded in biology. In the (...) present article, we challenge such a thesis. We provide evidence that theoretical biology operates with a plurality of equally valid organismic concepts, which imply different conclusions regarding the organismal status of a brain-dead patient. Moreover, the theoretical biology concepts of an organism are very distant from the view on an organism that appears by way of bioethicists theorizing on death. We conclude that if death is to be understood as the cessation of an organism, there is no single correct answer to the question of whether a brain-dead patient is alive or dead. (shrink)

We examine the epistemological foundations of a leading technique in the search for evidence of life on exosolar planets. Specifically, we consider the “transit method” for spectroscopic analysis of exoplanet atmospheres, and the practice of treating anomalous chemical compositions of the atmospheres of exosolar planets as indicators of the potential presence of life. We propose a methodology for ranking the anomalousness of atmospheres that uses the mathematical apparatus of support vector machines, and which aims to be agnostic with respect to (...) the particular chemical biosignatures of life. We argue that our approach is justified by an appeal to the “hinge” model of epistemic justification first proposed by as reported by Wittgenstein. We then compare our approach to previous work due to Walker et al. :779–824, 2018) and Cleland :722–729, 2019a; Does ‘life’ have a definition?, Cambridge University Press, New York, 2019b). (shrink)

This book provides a comprehensive overview of my recent theoretical work that aims to explain some of the more puzzling properties of life and mind, in particular agency, goal-directedness and consciousness. It contains published papers as well as new material. Table of contents: Preface - PART I: GROUNDWORK - 1. Introduction - 2. The basic mechanism - 3. Inclusive and extensive fitness - 4. Components of F and X - 5. The consequences: a preview - PART II: LIFE - 6. (...) What qualifies as life? - 7. Biological meaning - 8. Biological functions - PART III: MIND - 9. Minimal agency, goal-directedness and value - 10. Intentionality and meaning - 11. Language - 12. Consciousness - 13. The human self - PART IV: PHILOSOPHY - 14. Strong emergence - 15. The real, the true and the good - 16. Philosophical problems of consciousness - Epilogue - Appendix A: Summaries of computational simulations - Appendix B: Examples of minimal intentionality - References. -/- . (shrink)

This is a digest of how various researchers in biology and astrobiology have explored questions of what defines living organisms—definitions based on functions or structures observed in organisms, or on systems terms, or on mathematical conceptions like closure, chirality, quantum mechanics and thermodynamics, or on biosemiotics, or on Darwinian evolution—to clarify the field and make it easier for endeavors in artificial intelligence to make progress. Current ideas are described to promote work between astrobiologists and computer scientists, each concerned with living (...) organisms. A four-parameter framework is presented as a scaffold that is later developed into what machines lack to be considered alive: systems, evolution, energy and consciousness, and includes Jagers operators and the idea of dual closure. A novel definition of consciousness is developed which describes mental objects both with and without communicable properties, and this helps to clarify how consciousness in machines may be studied as an emergent process related to choice functions in systems. A perspective on how quantization, acting on nucleic acids, sets up natural limits to system behavior is offered as a partial address to the problem of biogenesis. (shrink)

Although the knowledge about biological systems has advanced exponentially in recent decades, it is surprising to realize that the very definition of Life keeps presenting theoretical challenges. Even if several lines of reasoning seek to identify the essence of life phenomenon, most of these thoughts contain fundamental problem in their basic conceptual structure. Most concepts fail to identify either necessary or sufficient features to define life. Here, we analyzed the main conceptual frameworks regarding theoretical aspects that have been supporting the (...) most accepted concepts of life, such as (i) the physical, (ii) the cellular and (iii) the molecular approaches. Based on an ontological analysis, we propose that Life should not be positioned under the ontological category of Matter. Yet, life should be better understood under the top-level ontology of “Process”. Exercising an epistemological approach, we propose that the essential characteristic that pervades each and every living being is the presence of organic codes. Therefore, we explore theories in biosemiotics and code biology in order to propose a clear concept of life as a macrocode composed by multiple inter-related coding layers. This way, as life is a sort of metaphysical process of encoding, the living beings became the molecular materialization of that process. From the proposed concept, we show that the evolutionary process is a fundamental characteristic for life’s maintenance but it is not necessary to define life, as many organisms are clearly alive but they do not participate in the evolutionary process (such as infertile hybrids). The current proposition opens a fertile field of debate in astrobiology, epistemology, biosemiotics, code biology and robotics. (shrink)

Aworkshop was held August 26–28, 2015, by the Earth- Life Science Institute (ELSI) Origins Network (EON, see Appendix I) at the Tokyo Institute of Technology. This meeting gathered a diverse group of around 40 scholars researching the origins of life (OoL) from various perspectives with the intent to find common ground, identify key questions and investigations for progress, and guide EON by suggesting a roadmap of activities. Specific challenges that the attendees were encouraged to address included the following: What key (...) questions, ideas, and investigations should the OoL research community address in the near and long term? How can this community better organize itself and prioritize its efforts? What roles can particular subfields play, and what can ELSI and EON do to facilitate research progress? (See also Appendix II.) The present document is a product of that workshop; a white paper that serves as a record of the discussion that took place and a guide and stimulus to the solution of the most urgent and important issues in the study of the OoL. This paper is not intended to be comprehensive or a balanced representation of the opinions of the entire OoL research community. It is intended to present a number of important position statements that contain many aspirational goals and suggestions as to how progress can be made in understanding the OoL. The key role played in the field by current societies and recurring meetings over the past many decades is fully acknowledged, including the International Society for the Study of the Origin of Life (ISSOL) and its official journal Origins of Life and Evolution of Biospheres, as well as the International Society for Artificial Life (ISAL). (shrink)

During the last decades the question of defining life has gained increased interest but, at the same time, the difficulty in reaching consensus on a possible answer has led many to skeptical positions. This, in turn, has raised a wider debate about why defining life is so hard and controversial. Such a debate introduces additional aspects to be considered, like the role and nature of a definition of life itself. In this paper, we will focus on those aspects, arguing that (...) progress can be made if we conceive definitions of life as open heuristic tools that contribute to develop specific research strategies in the biological sciences and, more generally, to increase our understanding of life’s complexity. In contrast with pragmatic or operationalist approaches, we will defend that definitions of life comprise a set of ontological assumptions, together with an inherent unifying vocation, so they should be subject to comparison and critical assessment, closely related to the success or failure of the corresponding research programs, but also to the success or failure in establishing well-grounded interconnections among the latter. We consider that the search for a more coherent, integrated and generalized theory of biology cannot be pursued without keeping an empirical standpoint, and the exercise of defining life should not be taken as an obstacle but as a valuable instrument to achieve that goal. (shrink)

This paper examines a fundamental philosophical difference between two radical postcognitivist theories that are usually assumed to offer the same view of cognition; namely the autopoietic theory and the enactive approach. The ways these two theories understand cognition, it is argued, are not compatible nor incompatible but rather incommensurable. The reason, so it is argued, is that while enactivism, following the traditional stance held by most of the cognitive theories, understands cognitive systems as constituting a natural kind, the autopoietic theory (...) understands them as constituting only a conventional kind. Additionally, the paper shows that AT’s conventionalist stance about cognition, far from being an undesirable or useless position, offers some methodological virtues that might be timely and welcome in the agitated and revolutionary climate of current cognitive science. (shrink)

This dissertation focuses on teleology and functions in biology. More precisely, it focuses on the scientific legitimacy of teleofunctional attributions and explanations in biology. It belongs to a multi-faceted debate that can be traced back to at least the 1970s. One aspect of the debate concerns the naturalization of functions. Most authors try to reduce, translate or explain functions and teleology in terms of efficient causes so that they find their place in the framework of the natural sciences. Our approach (...) here is radically different, as we question the premise that teleological explanations are disguised causal explanations. On the contrary, we defend that they are acceptable in natural sciences and in biology in particular. We challenge the idea that teleological explanations are immature causal explanations, as well as the idea that teleology and functions are some sort of intentional explanations. We therefore reject the accusations of anthropomorphism, vitalism and finalism. On the contrary, we defend that teleology, causality and intentionality correspond to different, autonomous and complementary modes of representation of the outside world. -/- ———[FRANÇAIS]——— -/- Ce travail de thèse porte sur la téléologie et les fonctions en biologie. Plus précisément, il porte sur la légitimité scientifique des attributions et des explications téléofonctionnelles en biologie. Il s’inscrit dans le cadre d’un débat à plusieurs facettes que l’on peut faire remonter au moins jusqu’aux années 1970 et qui est encore très actif aujourd’hui. L’un des aspects du débat porte sur la naturalisation des fonctions, c’est-à-dire sur la manière de les réduire, de les traduire ou de les expliciter en termes de causes efficientes de sorte qu’elles trouvent leur place dans le cadre des sciences de la nature. Notre approche ici est radicalement différente, car nous remettons en question la prémisse selon laquelle les explications téléologiques seraient des explications causales déguisées. Nous défendons au contraire qu’elles sont acceptables en tant que telles aussi bien de façon générale que dans le domaine scientifique et en particulier en biologie. De façon générale, nous remettons en question l’idée selon laquelle la pensée téléologique serait une pensée causale immature, ainsi que sa dépendance présumée vis-à-vis de la psychologie, c’est-à-dire de l’intentionnalité. Nous rejetons donc les accusations d’anthropomorphisme, de vitalisme et de finalisme formulées contre elle. Nous défendons au contraire que la téléologie, la causalité et l’intentionnalité correspondent à des modes différents, autonomes et complémentaires de représentation du monde extérieur. (shrink)

The philosophy of biology is witnessing an increasing enthusiasm for what can be called “individuals thinking”. Individuals thinking is a perspective on the metaphysics of biological entities according to which conceiving of them as individuals rather than kinds enables us to expose ongoing metaphysical debates as focusing on the wrong question, and to achieve better accounts of the metaphysics of biological entities. In this paper, I examine two cases of individuals thinking, the claim that species are individuals and the claim (...) that life on Earth is an individual. I argue that these claims fail to do the metaphysical work that one would want them to do. I highlight problems with the specific claims as well as with the general notion of ‘individual’, and argue that naturalistic metaphysicians of biology should think of the metaphysical status of theoretical entities, such as species and life, as fundamentally theory-dependent. This implies a metaphysical pluralism, that allows that in some theories species, life, and other such entities may feature as individuals, whereas in others they may feature as kinds. (shrink)

All the conserved detailed results of evolution stored in DNA must be read, transcribed, and translated via an RNAmediated process. This is required for the development and growth of each individual cell. Thus, all known living organisms fundamentally depend on these RNA-mediated processes. In most cases, they are interconnected with other RNAs and their associated protein complexes and function in a strictly coordinated hierarchy of temporal and spatial steps (i.e., an RNA network). Clearly, all cellular life as we know it (...) could not function without these key agents of DNA replication, namely rRNA, tRNA, and mRNA. Thus, any definition of life that lacks RNA functions and their networks misses an essential requirement for RNA agents that inherently regulate and coordinate (communicate to) cells, tissues, organs, and organisms. The precellular evolution of RNAs occurred at the core of the emergence of cellular life and the question remained of how both precellular and cellular levels are interconnected historically and functionally. RNA-networks andRNA-communication can interconnect these levels.With the reemergence of virology in evolution, it became clear that communicating viruses and subviral infectious genetic parasites are bridging these two levels by invading, integrating, coadapting, exapting, and recombining constituent parts in host genomes for cellular requirements in gene regulation and coordination aims. Therefore, a 21st century understanding of life is of an inherently social process based on communicating RNA networks, in which viruses and cells continuously interact. (shrink)

Symmetry-based explanations using symmetry breaking as the key explanatory tool have complemented and replaced traditional causal explanations in various domains of physics. The process of spontaneous SB is now a mainstay of contemporary explanatory accounts of large chunks of condensed-matter physics, quantum field theory, nonlinear dynamics, cosmology, and other disciplines. A wide range of empirical research into various phenomena related to symmetries and SB across biological scales has accumulated as well. Led by these results, we identify and explain some common (...) features of the emergence, propagation, and cascading of SB-induced layers across the biosphere. These features are predicated on the thermodynamic openness and intrinsic functional incompleteness of the systems at stake and have not been systematically analyzed from a general philosophical and methodological perspective. We also consider possible continuity of SB across the physical and biological world and discuss the connection between Darwinism and SB-based analysis of the biosphere and its history. (shrink)

The question of specific properties of life compared to nonliving things accompanied biology throughout its history. At times this question generated major controversies with largely diverging opinions. Basically, mechanistic thinkers, who tried to understand organismic functions in terms of nonliving machines, were opposed by those who tried to describe specific properties or even special forces being active within living entities. As this question included the human body, these controversies always have been of special relevance to our self-image and also touched (...) practical issues of medicine. During the second half of the twentieth century, it seemed to be resolved that organisms are explainable basically as physicochemical machines. Especially from the perspective of molecular biology, it seemed to be clear that organisms need to be explained solely by the chemical functions of their component parts, although some resistance to this view never ceased. This research program has been working quite successfully, so that science today knows a lot about the physiological and chemical processes within organisms. However, again new doubts arise questioning whether the mere continuation of this analytical approach will finally generate a fundamental understanding of living entities. At the beginning of the twenty-first century the quest for a new synthesis actually comes from analytical empiricists themselves. The hypothesis of the present paper is that empirical research has been developed far enough today, that it reveals by itself the materials and the prerequisites to understand more of the specific properties of life. Without recourse to mysterious forces, it is possible to generate answers to this age-old question, just using recent, empirically generated knowledge. This view does not contradict the results of reductionistic research, but rather grants them meaning within the context of organismic systems and also may increase their practical usefulness. Although several of these properties have been discussed before, different authors usually concentrated on a single one or some of them. The paper describes ten specific properties of living entities as they can be deduced from contemporary science. The aim is to demonstrate that the results of empirical research show both the necessity as well as the possibility of the development of a new conception of life to build a coherent understanding of organismic functions. (shrink)

Despite many attempts to achieve an adequate definition of living systems by means of a set of necessary and sufficient conditions, the opinion that such an enterprise is inexorably destined to fail is increasingly gaining support. However, we believe options do not just come down to either having faith in a future success or endorsing skepticism. In this paper, we aim to redirect the discussion of the problem by shifting the focus of attention from strict definitions towards a philosophical framework (...) that allows conceiving of living systems as a natural kind, but whereby natural kinds are not to be defined by fixed necessary and sufficient conditions. We argue for a property-cluster kind approach according to which living systems constitute a natural kind with vague boundaries, capable of changing, and whose members do not need to instantiate every property. We draw from Boyd’s homeostatic property-cluster theory and introduce two modifications, one regarding homeostatic mechanisms and another related to the scientific role of kinds. Thus, our view overcomes some difficulties of Boyd’s theory and we are able to account for the natural kindhood of living things. We also emphasize the most appealing features of our approach for specific research fields and address three objections to this sort of approach. (shrink)

Vitalism was long viewed as the most grotesque view in biological theory: appeals to a mysterious life-force, Romantic insistence on the autonomy of life, or worse, a metaphysics of an entirely living universe. In the early twentieth century, attempts were made to present a revised, lighter version that was not weighted down by revisionary metaphysics: “organicism”. And mainstream philosophers of science criticized Driesch and Bergson’s “neovitalism” as a too-strong ontological commitment to the existence of certain entities or “forces”, over and (...) above the system of causal relations studied by mechanistic science, rejecting the weaker form, organicism, as well. But there has been some significant scholarly “push-back” against this orthodox attitude, notably pointing to the 18th-century Montpellier vitalists to show that there are different historical forms of vitalism, including how they relate to mainstream scientific practice. Additionally, some trends in recent biology that run counter to genetic reductionism and the informational model of the gene present themselves as organicist. Here, we examine some cases of vitalism in the twentieth century and today, not just as a historical form but as a significant metaphysical and scientific model. We argue for vitalism’s conceptual originality without either reducing it to mainstream models of science or presenting it as an alternate model of science, by focusing on historical forms of vitalism, logical empiricist critiques thereof and the impact of synthetic biology on current theorizing of vitalism. (shrink)

To date, no definition of life has been unequivocally accepted by the scientific community. In frustration, some authors advocate alternatives to standard definitions. These include using a list of characteristic features, focusing on life’s effects, or categorizing biospheres rather than life itself; treating life as a fuzzy category, a process or a cluster of contingent properties; or advocating a ‘wait-and-see’ approach until other examples of life are created or discovered. But these skeptical, operational, and pluralistic approaches have intensified the debate, (...) rather than settled it. Given the failure of even these approaches, we advocate a new strategy. In this paper, we reverse the usual line of reasoning and argue that the “life problem” arises from thinking incorrectly about the nature of life. Scientists most often conceptualize life as a class or kind, with earthly life as a single instance of it. Instead, we advocate thinking about Earth’s Life as an individual, in the way that species are now thought to be. In this view, Life is a monophyletic clade that originated with a last universal common ancestor, and includes all its descendants. We can continue to use the category ‘life’ pragmatically to refer to similarities between various phenomena and Life. But the relevant similarities are a matter of interest and preference, not a matter of fact. The search for other life in the Universe, then, is merely a search for entities that resemble parts of Life in whatever sense astrobiologists find most appealing. This does not mean that the search for evolved complexity elsewhere in the universe or its creation in the lab are futile endeavors, but that debates over whether they count as ‘life’ are. Ironically, finally abandoning the concept ‘life’ may make our searches for evolved complexity more fruitful. We explain why. (shrink)

Despite many attempts to achieve an adequate definition of living systems by means of a set of necessary and sufficient conditions, the opinion that such an enterprise is inexorably destined to fail is increasingly gaining support. However, we believe options do not just come down to either having faith in a future success or endorsing skepticism. In this paper, we aim to redirect the discussion of the problem by shifting the focus of attention from strict definitions towards a philosophical framework (...) that allows conceiving of living systems as a natural kind, but whereby natural kinds are not to be defined by fixed necessary and sufficient conditions. We argue for a property-cluster kind approach according to which living systems constitute a natural kind with vague boundaries, capable of changing, and whose members do not need to instantiate every property. We draw from Boyd’s homeostatic property-cluster theory and introduce two modifications, one regarding homeostatic mechanisms and another related to the scientific role of kinds. Thus, our view overcomes some difficulties of Boyd’s theory and we are able to account for the natural kindhood of living things. We also emphasize the most appealing features of our approach for specific research fields and address three objections to this sort of approach. (shrink)

Whatever we take “life” to mean, it must involve an attempt to describe the objective reality beyond scientists’ biases. Traditionally, this is thought to involve comparing our scientific categories to “natural kinds.” But this approach has been tainted with an implicit metaphysics, inherited from Aristotle, that does not fit biological reality. In particular, we must accept that biological categories will never be specifiable in terms of necessary and sufficient conditions or shared underlying physical structures that produce clean boundaries. Biology blurs (...) all lines and failure to embrace this unique feature has blocked attempts to reach consensus on the meaning of “life.” Thus, while the three classical accounts all fall short of offering a complete definition, their advocates fail to realize that they share the same view of life’s ultimate, functional hallmark: its uniquely rich adaptive capacity. I develop an account of life as adaptive capacity that sidesteps debates about the relative importance of specific mechanisms and the precise location of boundaries to bring the three classical accounts together under a shared conceptual framework. (shrink)

In 2014, an international group of scholars from various fields analysed the “societal dimensions” of synthetic biology in an interdisciplinary summer school. Here, we report and discuss the biologists’ observations on the general perception of synthetic biology by non-biologists who took part in this event. Most attendees mainly associated synthetic biology with contributions from the best-known public figures of the field, rarely mentioning other scientists. Media extrapolations of those contributions appeared to have created unrealistic expectations and irrelevant fears that were (...) widely disconnected from the current research in synthetic biology. Another observation was that when debating developments in synthetic biology, semantics strongly mattered: depending on the terms used to present an application of synthetic biology, attendees reacted in radically different ways. For example, using the term “GMOs” rather than the term “genetic engineering” led to very different reactions. Stimulating debates also happened with participants having unanticipated points of view, for instance biocentrist ethicists who argued that engineered microbes should not be used for human purposes. Another communication challenge emerged from the connotations and inaccuracies surrounding the word “life”, which impaired constructive debates, thus leading to misconceptions about the abilities of scientists to engineer or even create living organisms. Finally, it appeared that synthetic biologists tend to overestimate the knowledge of non-biologists, further affecting communication. The motivation and ability of synthetic biologists to communicate their work outside their research field needs to be fostered, notably towards policymakers who need a more accurate and technical understanding of the field to make informed decisions. Interdisciplinary events gathering scholars working in and around synthetic biology are an effective tool in addressing those issues. (shrink)

Descartes is usually taken to be a strict reductionist, and he frequently describes his work in reductionist terms. This dissertation, however, makes the case that he is a nonreductionist in certain areas of his philosophy and natural philosophy. This might seem like simple inconsistency, or a mismatch between Descartes's ambitions and his achievements. I argue that here it is more than that: nonreductionism is compatible with his wider commitments, and allowing for irreducibles increases the explanatory power of his system. Moreover, (...) Descartes depends on nonreductionist knowledge and on irreducibles in order to maintain his epistemology and metaphysics. That is, there is more in the Cartesian world than mind, matter, and God. (shrink)

Consideration of the experimental activities carried out in one discipline, through the lens of another, can lead to novel insights. Here, we comment from a biological perspective upon experiments in quantum mechanics proposed by physicists that are likely to feasible in the near future. In these experiments, an entire living organism would be knowingly placed into a coherent quantum state for the first time, i.e. would be coerced into demonstrating quantum phenomena. The implications of the proposed experiment for a biologist (...) depend to an extent upon the outcomes. If successful, then the organism will have been temporarily in a state where it has an unmeasurable metabolism—not because a metabolic rate is undetectable, but because any attempt to measure it would automatically bring the organism out of the state. We argue that this would in essence represent a new category of cryptobiosis. Further, the organism would not necessarily retain all of the characteristics commonly attributed to living systems, unlike the currently known categories of cryptobiosis. If organisms can survive having previously been in a coherent state, then we must accept that living systems do not necessarily need to remain in a decoherent state at all times. This would be something new to biologists, even if it might seem trivial to physicists. It would have implications concerning the physical extremes organisms can tolerate, the search for extraterrestrial life, and our philosophical view of animation. (shrink)

Lipid vesicles are often used as compartment structures for preparing cell‐like systems and models of protocells, the hypothetical precursor structures of the first cells at the origin of life. Although the various artificially made vesicle systems are already remarkably complex, they are still very different from and much simpler than any known living cell. Nevertheless, the preparation and study of the structure and the dynamics of functionalized vesicle systems may contribute to a better understanding of biological cells, in particular of (...) the essential features of a living cell that are not found in the non‐living form of matter. The study of protocell models may possibly lead to a better understanding of the origin of the first cells. To avoid misunderstanding in this field of research, it would be useful if generally accepted definitions of terms like “artificial cells,” “synthetic cells,” “minimal cells,” “protocells,” and “primitive cells” exist. Editor's suggested further reading in BioEssaysSynthetic cells and organelles: compartmentalization strategies Abstract. (shrink)

In the dialectic of debates about the extension of life, one witnesses a predictably repeating pattern: one side appeals to a motley of variegated criteria for something’s qualifying as a living system, only to find an opposite side taking issue with the individual necessity or collective sufficiency of the proposed criteria. Some of these criteria tend to cluster with one another, while others do not: metabolism, growth and reproduction; self-organization and homeostasis; an ability to decrease internal entropy by the appropriation (...) of free energy; stimulus response suited to self-preservation and propagation; and adaptation. In competing approaches to the extension of life, these sundry criteria thus jockey for authority, with one group of theorists promoting some subset of them as essential for life, where the appeal to essence is as likely as not to be a simple modal sine qua non , and another denying that the nominated criteria are really necessary at all. The debate then stalls, because there seems to be no shared methodology for adjudicating such disputes. We may address this unhappy situation successfully by coming to appreciate that life is what we may call a core-dependent homonym. (shrink)

Radboud Universiteit Nijmegen, 06 september 2010.

We propose a framework for analyzing the development, operation and failure to survive of all things, living, non-living or organized groupings. This framework is a sequence of developments that improve survival capability. Framework processes range from origination of any entity/system, to the development of increased survival capability and development of life-forms and organizations that use intelligence. This work deals with a series of developmental changes that arise from the uncovering of emergent properties. The framework is intended to be general, but (...) we see a potential to apply it to scientific topics such as the exploration of the origin of life or the search for life beyond Earth, and to understand some biological issues in evolution and symbiosis, and also to apply to social systems that do not seem to be operating well, to determine their problems and correct them. (shrink)

En una serie de trabajos Carol Cleland ha argumentado por los últimos veinte años que la búsqueda de una definición de la vida es no solo inútil sino contraproducente. Una definición en términos de condiciones necesarias y suficientes nos podría cegar para la tarea mucho más importante de desarrollar una teoría universal de la vida. La principal justificación para este alegato es que la vida es una clase natural. Términos para clases naturales no poseen definiciones ideales, porque pretenden hacer referencia (...) a rasgos objetivos del mundo y no hacer explícito el contenido de nuestro pensamiento o lenguaje. Se argumenta aquí que la vida es, en efecto, una clase natural y, luego, la semántica para el término vida no puede darse por una definición ideal con condiciones necesarias y suficientes. Sin embargo, la semántica del término vida no excluye la posibilidad de hallar una ‘definición real’ adecuada de la esencia de la vida, esto es, de qué es la vida. Una definición real no es la enunciación del significado de un término sino de una esencia. (shrink)