Symbiosis plays a fundamental role in contemporary biology, as well as in recent thinking in philosophy of biology. The discovery of the importance and universality of symbiotic associations has brought new light to old debates in the field, including issues about the concept of biological individuality. An important aspect of these debates has been the formulation of the hologenome concept of evolution, the notion that holobionts are units of natural selection in evolution. This review examines the philosophical assumptions that (...) underlie recent proposal of the hologenome concept of evolution, and traces those debates back in time to their historical origins, to the moment when the connection between the topics of symbiosis and biological individuality first caught the attention of biologists. The review is divided in two parts. The first part explores the historical origins of the connection between the notion of symbiosis and the concept of biological individuality, and emphasizes the role of A. de Bary, R. Pound, A. Schneider and C. Merezhkowsky in framing the debate. The second part examines the hologenome concept of evolution and explores four parallelisms between contemporary debates and the debates presented in the first part of the essay, arguing that the different debates raised by the hologenome concept were already present in the literature. I suggest that the novelty of the hologenome concept of evolution lies in the wider appreciation of the importance of symbiosis for maintaining life on Earth as we know it. Finally, I conclude by suggesting the importance of exploring the connections among contemporary biology, philosophy of biology and history of biology in order to gain a better understanding of contemporary biology. (shrink)

The notion of a physiological individuals has been developed and applied in the philosophy of biology to understand symbiosis, an understanding of which is key to theorising about the major transition in evolution from multi-organismality to multi-cellularity. The paper begins by asking what such symbiotic individuals can help to reveal about a possible transition in the evolution of cognition. Such a transition marks the movement from cooperating individual biological cognizers to a functionally integrated cognizing unit. Somewhere along the way, (...) did such cognizing units simultaneously have cognizers as parts? Expanding upon the multiscale integration view of the Free Energy Principle, this paper develops an account of reciprocal integration, demonstrating how some coupled biological cognizing systems, when certain constraints are met, can result in a cognizing unit that is in ways greater than the sum of its cognizing parts. Symbiosis between V. Fischeri bacteria and the bobtail squid is used to provide an illustration this account. A novel manner of conceptualizing biological cognizers as gradient is then suggested. Lastly it is argued that the reason why the notion of ontologically nested cognizers may be unintuitive stems from the fact that our folk-psychology notion of what a cognizer is has been deeply influenced by our folk-biological manner of understanding biological individuals as units of reproduction. (shrink)

The theory of chemical symbiosis suggests that biological systems started with the collaboration of two polymeric molecules existing in early Earth: nucleic acids and peptides. Chemical symbiosis emerged when RNA-like nucleic acid polymers happened to fold into 3D structures capable to bind amino acids together, forming a proto peptidyl-transferase center. This folding catalyzed the formation of quasi-random small peptides, some of them capable to bind this ribozyme structure back and starting to form an initial layer that would produce (...) the larger subunit of the ribosome by accretion. TCS suggests that there is no chicken-and-egg problem into the emergence of biological systems as RNAs and peptides were of equal importance to the origin of life. Life has initially emerged when these two macromolecules started to interact in molecular symbiosis. Further, we suggest that life evolved into progenotes and cells due to the emergence of new layers of symbiosis. Mutualism is the strongest force in biology, capable to create novelties by emergent principles; on which the whole is bigger than the sum of the parts. TCS aims to apply the Margulian view of biology into the origins of life field. (shrink)

How does microbiota research impact our understanding of biological individuality? We summarize the interdisciplinary summer school on "Microbiota, Symbiosis and Individuality: Conceptual and Philosophical Issues" (July 2019), which was supported by a European Research Council starting grant project "Immunity, DEvelopment, and the Microbiota" (IDEM). The summer school centered around interdisciplinary group work on four facets of microbiota research: holobionts, individuality, causation, and human health. The conceptual discussion of cutting-edge empirical research provided new insights into microbiota and highlights the value (...) of incorporating into meetings experts from other disciplines, such as philosophy and history of science. (shrink)

A recent development in biology has been the growing acceptance that holobionts, entities comprised of symbiotic microbes and their host organisms, are widespread in nature. There is agreement that holobionts are evolved outcomes, but disagreement on how to characterize the operation of natural selection on them. The aim of this paper is to articulate the contours of the disagreement. I explain how two distinct foundational accounts of the process of natural selection give rise to competing views about evolutionary individuality.

One of intuitions driving the acceptance of a neat structured tree of life is the assumption that organisms and the lineages they form have somewhat stable spatial and temporal boundaries. The phenomenon of symbiosis shows us that such ‘fixist’ assumptions does not correspond to how the natural world actually works. The implications of lateral gene transfer (LGT) have been discussed elsewhere; I wish to stress a related point. I will focus on lateral function transfer (LFT) and will argue, using (...) examples of what many would call ‘superorganisms’, that the emergence of symbiotic individuals revives the importance of functional and adaptationist thinking in how we conceptualize the lineages of biological individuals. The consequence of the argument is that, if we really want to hold onto tree of life thinking, we had better accept that new saplings appear and disappear all the time. (shrink)

Analytic metaphysics has recently discovered biology as a means of grounding metaphysical theories. This has resulted in long-standing metaphysical puzzles, such as the problems of personal identity and material constitution, being increasingly addressed by appeal to a biological understanding of identity. This development within metaphysics is in significant tension with the growing tendency amongst philosophers of biology to regard biological identity as a deep puzzle in its own right, especially following recent advances in our understanding of symbiosis, the evolution (...) of multi-cellular organisms and the inherently dynamical character of living systems. Moreover, and building on these biological insights, the broadly substance ontological framework of metaphysical theories of biological identity appears problematic to a growing number of philosophers of biology who invoke process ontology instead. This volume addresses this tension, exploring to what extent it can be dissolved. For this purpose, the volume presents the first selection of essays exclusively focused on biological identity and written by experts in metaphysics, the philosophy of biology and biology. The resulting cross-disciplinary dialogue paves the way for a convincing account of biological identity that is both metaphysically constructive and scientifically informed, and will be of interest to metaphysicians, philosophers of biology and theoretical biologists. (shrink)

The original article has been corrected. Several typos in the article have been corrected.

E. O. Wilson (1974: 54) describes the problem that social organisms pose: “On what bases do we distinguish the extremely modified members of an invertebrate colony from the organs of a metazoan animal?” This framing of the issue has inspired many to look more closely at how groups of organisms form and behave as emergent individuals. The possible existence of “superorganisms” test our best intuitions about what can count and act as genuine biological individuals and how we should study them. (...) As we will discuss, colonies of certain organisms display many of the properties that we usually reserve only to individual organisms. Although there is good reason to believe that many social insects form genuine emergent biological individuals, the conclusion offered here is of a slightly different sort. I will argue that to understand some social insects' interactions and the emergent traits they give rise to, it may be helpful to shift our understanding from a community-level approach to an ecosystem-level approach. I will argue that viewing certain insect colonies (termites) as parts of ecosystems allows us to better understand some of the adaptations that have emerged from their evolution. (shrink)

Analytic metaphysics has recently discovered biology as a means of grounding metaphysical theories. This has resulted in long-standing metaphysical puzzles, such as the problems of personal identity and material constitution, being increasingly addressed by appeal to a biological understanding of identity. This development within metaphysics is in significant tension with the growing tendency amongst philosophers of biology to regard biological identity as a deep puzzle in its own right, especially following recent advances in our understanding of symbiosis, the evolution (...) of multi-cellular organisms and the inherently dynamical character of living systems. Moreover, and building on these biological insights, the broadly substance ontological framework of metaphysical theories of biological identity appears problematic to a growing number of philosophers of biology who invoke process ontology instead. This volume addresses this tension, exploring to what extent it can be dissolved. For this purpose, the volume presents the first selection of essays exclusively focused on biological identity and written by experts in metaphysics, the philosophy of biology and biology. The resulting cross-disciplinary dialogue paves the way for a convincing account of biological identity that is both metaphysically constructive and scientifically informed, and will be of interest to metaphysicians, philosophers of biology and theoretical biologists. (shrink)

Biological species are often taken as counterexamples to essentialist accounts of natural kinds. Essentialists like Ellis (2001) agree with nominalists that because biological kinds evolve, any distinctions between kinds of biological kind must ultimately be arbitrary. The resulting vagueness in the extension of natural kind predicates in the case of species has led to the claim that species ought to be construed as individuals rather than kinds (Ghiselin 1974, 1987; Hull 1976, 1978). I examine the possibility that causal features extrinsic (...) to the properties of natural kinds are responsible for establishing the unity of the properties of a natural kind. I reject the intuitive idea that laws of nature might act as such an external mechanism because this would entail an account of ceteris paribus biological laws, where there are no plausible truthmakers in terms of kinds or properties. I suggest instead that symbiosis is a plausible external causal mechanism, which explains the evolution of homeostasis in natural kind clusters. This involves the acceptance of an expanded account of evolutionary development as cooperative symbiosis. (shrink)

I formulate in relational terms the ubiquitous biological interaction of symbiosis. I explicate the topology of the different modes of relational interactions of (M, R)-networks, the entailment diagrams that model the host and the symbiont. These modes all have biological realizations as various categories of symbiotic relationships, ranging from mutualism to parasitism to infection.

Robustness is a fundamental property of biological systems, observed ubiquitously across species and at different levels of organization from gene regulation to ecosystem. The theory of biological robustness argues that robustness fosters evolv-ability and that together they entail various tradeoffs as well as characteristic architectures and mechanisms. We argue that classes of biological systems have evolved to enhance their robustness by extending their system boundary through a series of symbioses with foreign biological entities . A series of major biological innovations (...) has been achieved by events consistent with this framework: horizontal gene transfer, serial endosymbiosis, oocytes-mediated vertical infection, and host-symbiont mutualism for bacterial flora. Self-extending symbiosis contributes to robustness because symbiotic foreign biological entities can enhance the adaptative capacity of the system against environmental perturbations as well as contribute novel functions. In addition, evolutionary history indicates that the degree of symbiosis achieved has substantially changed from tight integration into the genome to loose integration as bacterial flora . The most dramatic example can be seen in the symbiosis of host immune system and bacterial flora in which substantial function of host defense depends on the proper maintenance of bacterial flora and its adaptive capability. Biological systems following this type of evolutionary path might have attained high levels of functionality, robustness, and evolvability. Thus, robustness, evolution, and self-extending symbiosis may form essential system principles for biology. (shrink)

Natural selection is commonly interpreted as the fundamental mechanism of evolution. Questions about how selection theory can claim to be the all-sufficient explanation of evolution often go unanswered by today's neo-Darwinists, perhaps for fear that any criticism of the evolutionary paradigm will encourage creationists and proponents of intelligent design.In Biological Emergences, Robert Reid argues that natural selection is not the cause of evolution. He writes that the causes of variations, which he refers to as natural experiments, are independent of natural (...) selection; indeed, he suggests, natural selection may get in the way of evolution. Reid proposes an alternative theory to explain how emergent novelties are generated and under what conditions they can overcome the resistance of natural selection. He suggests that what causes innovative variation causes evolution, and that these phenomena are environmental as well as organismal.After an extended critique of selectionism, Reid constructs an emergence theory of evolution, first examining the evidence in three causal arenas of emergent evolution: symbiosis/association, evolutionary physiology/behavior, and developmental evolution. Based on this evidence of causation, he proposes some working hypotheses, examining mechanisms and processes common to all three arenas, and arrives at a theoretical framework that accounts for generative mechanisms and emergent qualities. Without selectionism, Reid argues, evolutionary innovation can more easily be integrated into a general thesis. Finally, Reid proposes a biological synthesis of rapid emergent evolutionary phases and the prolonged, dynamically stable, non-evolutionary phases imposed by natural selection. (shrink)

A correspondence allows application of Landau and Lifshitz’ formulation of Le Chatelier’s principle from statistical physics to a simple 2-D model of biological symbiosis. The insight: symbionts stabilize the occupation of narrow peaks on fitness landscape.

A crucial question for a process view of life is how to identify a process and how to follow it through time. The genidentity view can contribute decisively to this project. It says that the identity through time of an entity X is given by a well-identified series of continuous states of affairs. Genidentity helps address the problem of diachronic identity in the living world. This chapter describes the centrality of the concept of genidentity for David Hull and proposes an (...) extension of Hull’s view to the ubiquitous phenomenon of symbiosis. Finally, using immunology as a key example, it shows that the genidentity view suggests that the main interest of a process approach is epistemological rather than ontological and that its principal claim is one of priority, namely that processes precede and define things, and not vice versa. (shrink)

This chapter introduces the main research schools and paradigms along which the field of evolutionary biology has been developing. Evolutionary thinking was originally founded upon the Neo-Darwinian paradigm that combines the teachings of traditional Darwinism with those of the Modern Synthesis. The Neo-Darwinian paradigm has since further diversified into the Micro-, Meso-, and Macroevolutionary schools, and it has also started to integrate the school of Ecology. Together, these schools establish the paradigm called Ecological Evolutionary Developmental Biology (Eco-Evo-Devo). A final school (...) studies Reticulate Evolution as it occurs by means of symbiosis, symbiogenesis, lateral gene transfer, infective heredity, and hybridization. This chapter reviews the major tenets and points of differentiation that exist between these distinct evolution schools. The chapter ends by looking into how evolution can be defined and how distinct units, levels, and mechanisms underlie theorizing on evolutionary hierarchies and evolutionary causation. The following chapter examines how the different evolution schools are implemented into the symbolic sciences. (shrink)

Emphatic claims of a “microbiome revolution” aside, the study of the gut microbiota and its role in organismal development and evolution is a central feature of so-called postgenomics; namely, a conceptual and/or practical turn in contemporary life sciences, which departs from genetic determinism and reductionism to explore holism, emergentism and complexity in biological knowledge-production. This paper analyses the making of postgenomic knowledge about developmental symbiosis in Drosophila melanogaster by a specific group of microbiome scientists. Drawing from both practical philosophy (...) of science and Science and Technology Studies, the paper documents epistemological questions of artefactuality and representativeness of model organisms as they emerge in the day-to-day labour producing and being produced by the “microbiome revolution." Specifically, the paper builds on all the written and editorial exchanges involved in the troubled publication of a research paper studying the symbiotic role of the microbiota in the flies’ development. These written materials permit us to delimit the network of justifications, evidence, standards of knowledge-production, trust in the tools and research designs that make up the conditions of possibility of a postgenomic fact. More than reframing the organism as a radically novel multiplicity of reactive genomes, we conclude, doing postgenomic research on the microbiota and symbiosis means producing a story that deviates from the scripts embedded into the sociotechnical experimental systems of post-Human Genome Project life sciences. (shrink)

Since the 1950s, the common view of development has been internalist: development is seen as the result of the unfolding of potentialities already present in the egg cell. In this article, I show that this view is incorrect because of the crucial influence of the environment on development. I focus on a fascinating example, that of the role played by symbioses in development, especially bacterial symbioses, a phenomenon found in virtually all organisms (plants, invertebrates, and vertebrates). I claim that we (...) must consequently modify our conception of the boundaries of the developing entity, and I show how immunology can help us in accomplishing this task. I conclude that the developing entity encompasses many elements traditionally seen as “foreign,” while I reject the idea that there is no possible distinction between the organism and its environment. (shrink)

The paper outlines the contours of an organizational perspective on extended inheritance. Based on theoretical studies about biological organization and extended physiology, this perspective allows for the conception of extended biological legacies while keeping a theoretically indispensable distinction between biological systems and their environment. In this context, the line of demarcation between these systems and their surroundings is modelled on an organizational criterion and on the related conceptual distinction between organizational constraints, whose specific role is to harness flows of matter (...) and energy across generations of composite biological systems, and resources exploited by those systems. Biological legacies are restricted to persisting constitutive elements responsible for the reoccurrence of organizational constraints in a given environment. The case of symbiotic transmission is presented as a paradigmatic system illustrating the main proposed conceptual clarifications. (shrink)

The hologenome concept of evolution is a hypothesis about the evolution of animals and plants. It asserts that the evolution of animals and plants was partially triggered by their interactions with their symbiotic microbiomes. In that vein, the hologenome concept posits that the holobiont (animal host + symbionts of the microbiome) is a unit of selection. -/- The hologenome concept has been severely criticized on the basis that selection on holobionts would only be possible if there were a tight transgenerational (...) host-genotype-to-symbiont-genotype connection. As our current evidence suggests that this is not the case for most of the symbiont species that compose the microbiome of animals and plants, the opportunity for holobiont selection is very low in relation to the opportunity for selection on each of the species that compose the host microbiome. Therefore, holobiont selection will always be disrupted ‘from below’, by selection on each of the species that compose the microbiome. -/- This thesis constitutes a conceptual effort to defend philosophically the hologenome concept. I argue that the criticism according to which holobiont selection requires tight transgenerational host-genotype-to-symbiont-genotype connection is grounded on a metaphysical view of the world according to which the biological hierarchy needs to be nested, such that each new level of selection includes every entity from below. Applied to hologenomes, it entails that the hologenome is a collection of genomes, and selection of hologenomes is assumed to entail cospeciation of the host with the species that constitute its microbiome. -/- Against that interpretation, I propose the ‘stability of traits’ account, according to which hologenome evolution is the result of the action of natural selection in a non-nested hierarchical world. In that vein, hologenome evolution does not entail cospeciation, and thus it does not require tight transgenerational host-genotype-to-symbiont-genotype connection. By embracing a multilevel selection perspective, I argue that hologenome evolution results from the simultaneous action of natural selection on each of the lineages that compose the microbiome, and on the assemblage composed by the host genome plus the functional traits of its microbiome. Hologenome selection occurs when the evolution of the traits of the microbiome result from their effects on the fitness of the host, and it can take the form of multilevel selection 1, or multilevel selection 2. In both cases, hologenome selection entails the evolution of microbiome traits, as well as evolution of the host genome, rather than cospeciation of lineages. (shrink)

Our intuitive assumption that only organisms are the real individuals in the natural world is at odds with developments in cell biology, ecology, genetics, evolutionary biology, and other fields. Although organisms have served for centuries as nature's paradigmatic individuals, science suggests that organisms are only one of the many ways in which the natural world could be organized. When living beings work together--as in ant colonies, beehives, and bacteria-metazoan symbiosis--new collective individuals can emerge. In this book, leading scholars consider (...) the biological and philosophical implications of the emergence of these new collective individuals from associations of living beings. The topics they consider range from metaphysical issues to biological research on natural selection, sociobiology, and symbiosis. (shrink)

In a macroevolutionary timescale, evolvability itself evolves. Lineages are sorted based on their ability to generate adaptive novelties, which leads to the optimization of their genotype-phenotype map. The system of translation of genetic or epigenetic changes to the phenotype may reach significant horizontal and vertical complexity, and may even exhibit certain aspects of learning behaviour. This continuously evolving semiotic system probably enables the origin of complex yet functional and internally compatible adaptations. However, it also has a second, “darker”, side. As (...) was pointed out by several authors, the same process gradually reduces the probability of the origination of significant evolutionary novelties. In a similar way to the evolution of societies, teachings, or languages, in which the growing number of internal linkages gradually solidifies their overall structure and the structure or interpretation of their constitutive elements, the evolutionary potential of lineages decreases during biological evolution. Possible adaptations become limited to small “peripheral” modifications. According to the Frozen Evolution theory, some of the proximate causes of this “macroevolutionary freezing” are more pronounced or present exclusively in sexual lineages. Sorting based on the highest evolvability probably leads to the establishment of certain structural features of complex organisms, e.g. the modular character of their development and morphology. However, modules also “macroevolutionary freeze” whereas the hypothetical “thawing” of modules or their novel adaptive combinations becomes rarer and rarer. Some possible ways out of this dead end include the rearrangement of individual development, e.g. neoteny, radical simplification, i.e. sacculinization, and transition to a higher level of organization, e.g. symbiosis or symbiogenesis. The evolution of evolvability is essentially a biosemiotic process situated at the intersection of the genocentric modern synthesis and the evo-devo-centric extended synthesis. Therefore, evolvability may eventually connect these three not necessarily contradictory approaches. (shrink)

Since the beginning of time, the pre-biological and the biological world have seen a steady increase in complexity of form and function based on a process of combination and re-combination. The current modern synthesis of evolution known as the neo-Darwinian theory emphasises population genetics and does not explain satisfactorily all other occurrences of evolutionary novelty. The authors suggest that symbiosis and hybridisation and the more obscure processes such as polyploidy, chimerism and lateral transfer are mostly overlooked and not featured (...) sufficiently within evolutionary theory. They suggest, therefore, a revision of the existing theory including its language, to accommodate the scientific findings of recent decades. (shrink)

Our intuitive assumption that only organisms are the real individuals in the natural world is at odds with developments in cell biology, ecology, genetics, evolutionary biology, and other fields. Although organisms have served for centuries as nature’s paradigmatic individuals, science suggests that organisms are only one of the many ways in which the natural world could be organized. When living beings work together—as in ant colonies, beehives, and bacteria-metazoan symbiosis—new collective individuals can emerge. In this book, leading scholars consider (...) the biological and philosophical implications of the emergence of these new collective individuals from associations of living beings. The topics they consider range from metaphysical issues to biological research on natural selection, sociobiology, and symbiosis. -/- The contributors investigate individuality and its relationship to evolution and the specific concept of organism; the tension between group evolution and individual adaptation; and the structure of collective individuals and the extent to which they can be defined by the same concept of individuality. These new perspectives on evolved individuality should trigger important revisions to both philosophical and biological conceptions of the individual. -/- Contributors: Frédéric Bouchard, Ellen Clarke, Jennifer Fewell, Andrew Gardner, Peter Godfrey-Smith, Charles J. Goodnight, Matt Haber, Andrew Hamilton, Philippe Huneman, Samir Okasha, Thomas Pradeu, Scott Turner, Minus van Baalen. (shrink)

Written for non-experts, this volume introduces the mechanisms that underlie reticulate evolution. Chapters are either accompanied with glossaries that explain new terminology or timelines that position pioneering scholars and their major discoveries in their historical contexts. The contributing authors outline the history and original context of discovery of symbiosis, symbiogenesis, lateral gene transfer, hybridization or divergence with gene flow, and infectious heredity. By applying key insights from the areas of molecular (phylo)genetics, microbiology, virology, ecology, systematics, immunology, epidemiology and computational (...) science, they demonstrate how reticulate evolution impacts successful survival, fitness and speciation. Reticulate evolution brings forth a challenge to the standard Neo-Darwinian framework, which defines life as the outcome of bifurcation and ramification patterns brought forth by the vertical mechanism of natural selection. Reticulate evolution puts forward a pattern in the tree of life that is characterized by horizontal mergings and lineage crossings induced by symbiosis, symbiogenesis, lateral gene transfer, hybridization or divergence with gene flow, and infective heredity, making the “tree of life” look more like a “web of life.” On an epistemological level, the various means by which hereditary material can be transferred horizontally challenges our classic notions of units and levels of evolution, fitness, modes of transmission, linearity, communities, and biological individuality. The case studies presented examine topics including the origin of the eukaryotic cell and its organelles through symbiogenesis; the origin of algae through primary and secondary symbiosis and dinoflagellates through tertiary symbiosis; the superorganism and holobiont as units of evolution; how endosymbiosis induces speciation in multicellular life forms; transferrable and non-transferrable plasmids and how they symbiotically interact with their host; the means by which pro- and eukaryotic organisms transfer genes laterally (bacterial transformation, transduction and conjugation as well as transposons and other mobile genetic elements); hybridization and divergence with gene flow in sexually-reproducing individuals; current (human) microbiome and viriome studies that impact our knowledge concerning the evolution of organismal health and acquired immunity; and how symbiosis and symbiogenesis can be modelled in computational evolution. (shrink)

While examples of bacteria benefiting eukaryotes are increasingly documented, studies examining effects of eukaryote hosts on microbial fitness are rare. Beneficial bacteria are often called “mutualistic” even if mutual reciprocity of benefits has not been demonstrated and despite the plausibility of other explanations for these microbes' beneficial effects on host fitness. Furthermore, beneficial bacteria often occur in diverse communities, making mutualism both empirically and conceptually difficult to demonstrate. We suggest reserving the terms “mutualism” and “parasitism” for pairwise interactions where the (...) relationship is largely independent of other species and can be verified by measuring the fitness effect experienced by both partners. In hosts with diverse microbial communities, we propose re‐formulating some of the essential questions of symbiosis research – e.g. concerning specificity, transmission mode, and common evolutionary fates – as questions of community ecology and ecosystem function, allowing important biological interactions to be investigated without making assumptions about reciprocity. Understanding the fitness of host‐associated bacteria is a crucial component of investigations into the role of microbes in eukaryote evolution. (shrink)

This paper introduces Deleuze and Guattari's assemblage theory into the contemporary biological context. I begin by laying out at some length what I take to be the defining features of Deleuze and Guattari's theory of assemblage. I consider this to be a worthwhile endeavour in its own right, and so dedicate a large portion of this paper to producing a clear account of what it is that characterises an assemblage. Then I provide a reading of Deleuze and Guattari's critical conception (...) of the organism as a kind of assemblage typified by an especially restrictive, self-regulating form of functional integration. This restrictiveness comprises what I take to be the first pole of organic life. Then I reconsider Deleuze and Guattari's positive comments about ‘non-organic life’ in this context, as a feature internal to the organisation of organic life instead of something to be set against it. I theorise this mostly in terms of symbiosis. I take the significance of symbiosis, consisting in what Deleuze and Guattari call ‘shared deterritorialisation’, to comprise the second pole of organic life. I conclude the paper with a brief discussion of how Deleuze and Guattari's assemblage-based conception of organism might be thought to anticipate and accommodate some of the contemporary research on biological individuality. (shrink)

Symbiosis is a biological phenomenon in which two dissimilar organisms coexist for mutual subsistence. The concept of symbiosis can be employed to foster mutual learning. In this paper, the...

Religion persists, even within enlightened secular society, because it has adaptive functions. In particular, Ralph Wendell Burhoe's theory holds that religion is the repository of cultural wisdom that most encourages mutual altruism among nonkin, long-term social survival, and human progress. This article suggests a variant of Burhoe's rationalized naturalistic view. Cognitive theism is a proposal that secularists sometimes take religion on its own terms by suspending disbelief about God. If we consider particular human capacities and limitations in memory, perception, personality, (...) and motivation, the regulated “mind expansion” of cognitive theism may help us to evaluate, coordinate, and invigorate things in a modern environment. In this environment, communicative and travel technologies have led to a high loading of consciousness with a historically unusual diverse range of experiences and responsibilities, a high rate of cultural change relative to biological evolution, and a tendency to factionalize. Burhoe's extension of the concept of symbiosis to the coevolution of culture and genes is modified here in recognition of individual differences and of individuals' potential for choosing strategies, recombining in groups, and learning. In human biocultural symbiont pools, cultural phenomena can evolve while changing partners in a dance with genetic substrates, a dance that broadly supports these substrates. In the context of diversity and incessant change in a large predominantly secular community, Judeo-Christian monotheism can have a valuable advisory unifying function. (shrink)

Holobionts are symbiotic assemblages composed by a host plus its microbiome. The status of holobionts as individuals has recently been a subject of continuous controversy, which has given rise to two main positions: on the one hand, holobiont advocates argue that holobionts are biological individuals; on the other, holobiont detractors argue that they are just mere chimeras or ecological communities, but not individuals. Both parties in the dispute develop their arguments from the framework of the philosophy of biology, in terms (...) of what it takes for a “conglomerate” to be considered an interesting individual from a biological point of view. However, the debates about holobiont individuality have important ontological implications that have remained vaguely explored from a metaphysical framework. The purpose of this paper is to cover that gap by presenting a metaphysical approach to holobionts individuality. Drawing upon a conception of natural selection that puts the focus on the transgenerational recurrence of the traits and that supports the thesis that holobionts are units of selection, we argue that holobionts bear emergent traits and exert downward powers over the entities that compose them. In this vein, we argue, a reasonable argument can be made for conceiving holobionts as emergent biological individuals. (shrink)

This collection of essays explores the metaphysical thesis that the living world is not made up of substantial particles or things, as has often been assumed, but is rather constituted by processes. The biological domain is organised as an interdependent hierarchy of processes, which are stabilised and actively maintained at different timescales. Even entities that intuitively appear to be paradigms of things, such as organisms, are actually better understood as processes. Unlike previous attempts to articulate processual views of biology, which (...) have tended to use Alfred North Whitehead’s panpsychist metaphysics as a foundation, this book takes a naturalistic approach to metaphysics. It submits that the main motivations for replacing an ontology of substances with one of processes are to be found in the empirical findings of science. Biology provides compelling reasons for thinking that the living realm is fundamentally dynamic, and that the existence of things is always conditional on the existence of processes. The phenomenon of life cries out for theories that prioritise processes over things, and it suggests that the central explanandum of biology is not change but rather stability, or more precisely, stability attained through constant change. This edited volume brings together philosophers of science and metaphysicians interested in exploring the consequences of a processual philosophy of biology. The contributors draw on an extremely wide range of biological case studies, and employ a process perspective to cast new light on a number of traditional philosophical problems, such as identity, persistence, and individuality. (shrink)

This anthology collects some of the most important papers on what is believed to be the major force in evolution, natural selection. An issue of great consequence in the philosophy of biology concerns the levels at which, and the units upon which selection acts. In recent years, biologists and philosophers have published a large number of papers bearing on this subject. The papers selected for inclusion in this book are divided into three main sections covering the history of the subject, (...) explaining its conceptual foundations, and focusing on kin and group selection and higher levels of selection.One of the book's interesting features is that it draws together material from the biological and philosophical literatures. The philosophical literature, having thoroughly absorbed the biological material, now offers conceptual tools suitable for the reworking of the biological arguments. Although a full symbiosis has yet to develop, this anthology offers a unique resource for students in both biology and philosophy.Robert N. Brandon is Professor in the Philosophy Department, Duke University. Richard M. Burian is Professor of Philosophy and Department Chairman, Virginia Polytechnic Institute and State University.A Bradford Book. (shrink)

In a warm and enjoyable dialogue the meaning of health, in its fullest sense, becomes a philosophical issue as much as a biological. For isn't the essence of health a general sense of well-being? Health can be seen as reflecting satisfaction with our quality of life; but how do we achieve that? Here, a character who is heading off for a job teaching health has an extended conversation with a trusted mentor, and they test various definitions, various visions, and some (...) of the infinite possibilities of the idea of health, in the process coming to a deeper and more invigorating understanding of life itself. They arrive at the notion of symbiosis - a living together to the advantage of each. And isn't a good conversation a sort of living together to the advantage of each? In such dialogue, we engage with our hearts and minds. When are we more alive than that? What is the peak of health if not this life, this engagement? The two friends want to know what health is. But they want more: They want to be healthy. They see three basic types of health - bodily, mental, and societal. These three types affect one another. How they affect one another matters in a critical way. But there is more. A friendly conversation allows special access to what is critical. Our guard is down in such a conversation. We are less likely to be defensive. We are more likely to keep our minds open and clear. We are likely to feel the confidence it takes to learn. (shrink)

Forty years’ experience as a bacterial geneticist has taught me that bacteria possess many cognitive, computational and evolutionary capabilities unimaginable in the first six decades of the twentieth century. Analysis of cellular processes such as metabolism, regulation of protein synthesis, and DNA repair established that bacteria continually monitor their external and internal environments and compute functional outputs based on information provided by their sensory apparatus. Studies of genetic recombination, lysogeny, antibiotic resistance and my own work on transposable elements revealed multiple (...) widespread bacterial systems for mobilizing and engineering DNA molecules. Examination of colony development and organization led me to appreciate how extensive multicellular collaboration is among the majority of bacterial species. Contemporary research in many laboratories on cell–cell signaling, symbiosis and pathogenesis show that bacteria utilise sophisticated mechanisms for intercellular communication and even have the ability to commandeer the basic cell biology of ‘higher’ plants and animals to meet their own needs. This remarkable series of observations requires us to revise basic ideas about biological information processing and recognise that even the smallest cells are sentient beings. Previous article in issue. (shrink)

The question “What is an organism?”, formerly considered as essential in biology, has now been increasingly replaced by a larger question, “What is a biological individual?”. On the grounds that i) individuation is theory-dependent, and ii) physiology does not offer a theory, biologists and philosophers of biology have claimed that it is the theory of evolution by natural selection which tells us what counts as a biological individual. Here I show that one physiological field, immunology, offers a theory, which makes (...) possible a biological individuation based on physiological grounds. I give a new answer to the question of the individuation of an organism by linking together the evolutionary and the immunological approaches to biological individuation. (shrink)

Forty years’ experience as a bacterial geneticist has taught me that bacteria possess many cognitive, computational and evolutionary capabilities unimaginable in the first six decades of the twentieth century. Analysis of cellular processes such as metabolism, regulation of protein synthesis, and DNA repair established that bacteria continually monitor their external and internal environments and compute functional outputs based on information provided by their sensory apparatus. Studies of genetic recombination, lysogeny, antibiotic resistance and my own work on transposable elements revealed multiple (...) widespread bacterial systems for mobilizing and engineering DNA molecules. Examination of colony development and organization led me to appreciate how extensive multicellular collaboration is among the majority of bacterial species. Contemporary research in many laboratories on cell–cell signaling, symbiosis and pathogenesis show that bacteria utilise sophisticated mechanisms for intercellular communication and even have the ability to commandeer the basic cell biology of ‘higher’ plants and animals to meet their own needs. This remarkable series of observations requires us to revise basic ideas about biological information processing and recognise that even the smallest cells are sentient beings. (shrink)

Given immunity’s general role in the organism’s economy—both in terms of its internal environment as well as mediating its external relations—immune theory has expanded its traditional formulation of preserving individual autonomy to one that includes accounting for nutritional processes and symbiotic relationships that require immune tolerance. When such a full ecological alignment is adopted, the immune system becomes the mediator of both defensive and assimilative environmental intercourse, where a balance of immune rejection and tolerance governs the complex interactions of the (...) organism’s ecological relationships. Accordingly, immunology, which historically had affiliated with the biology of individuals, now becomes a science concerned with the biology of communities. With this translocation, the ontological basis of the organism is undergoing a profound change. Indeed, the recent recognition of the ubiquity of symbiosis has challenged the traditional notions of biological individuality and requires a shift in the metaphysics undergirding biology, in which a philosophy of the organism must be characterized by ecological dialectics “all-the-way-down.”. (shrink)

If we are to ensure the persistence of species in an increasingly warm world, of interest is the identification of drivers that affect the ability of an organism to resist thermal stress. Underpinning any organism's capacity for resistance is a complex interplay between biological and physical factors occurring over multiple scales. Tropical coral reefs are a unique system, in that their function is dependent upon the maintenance of a coral–algal symbiosis that is directly disrupted by increases in water temperature. (...) A number of physical factors have been identified as affecting the biological responses of the coral organism under broadscale thermal anomalies. One such factor is water flow, which is capable of modulating both organismal metabolic functioning and thermal environments. Understanding the physiological and hydrodynamic drivers of organism response to thermal stress improves predictive capabilities and informs targeted management responses, thereby increasing the resilience of reefs into the future. (shrink)

Global human population expansion is rooted in a remarkably successful evolutionary innovation. The neolithic transformation of the natural world gave rise to a symbiosis between humans and their domesticated plant and animal partners that will expand from a current 20 per cent to 60 percent of terrestrial biomass by the middle of the coming century. Such an increase must necessarily be accompanied by a concomitant decrease in wildlife biomass. We suggest that current trends in population growth are unlikely to (...) abate for three reasons: first, there are intrinsic biological pressures to reproduce regardless of social engineering; second, the character of the domestic alliance makes it a formidable competitor to wildlife; and third, the timeframe before population doubling is, from a biological perspective, virtually instantaneous. This paper draws from a wide body of research in the biological and social sciences. We neither condone nor endorse this picture of inexorable population increase. Rather, we appeal for a change in the nature of the discussion of population among environmentalists, to focus on the question of how best to manage what wildlife will be left on the margins of a domesticated world. (shrink)

Much of the literature directed at the Extended Mind Thesis has revolved around parity issues, focussing on the problem of how to individuate the functional roles and on the relevance of these roles for the production of human intelligent behaviour. Proponents of EMT have famously claimed that we shouldn’t take the location of a process as a reliable indicator of the mechanisms that support our cognitive behaviour. This functionalist understanding of cognition has however been challenged by opponents of EMT [such (...) as Rupert ; Adams & Aizawa ], who have claimed that differences between internal, biological processes and putatively extended ones not only exist but are actually crucial to undermine the idea that inner and outer are functionally equivalent. This debate about how to individuate the functional roles has led to a treacherous stand-off, in which proponents of EMT have been trapped under the persistent accusation of causal/constitution conflation. My strategy for responding to this charge is to look precisely at those functional differences highlighted by critics of EMT. I reckon that extended cognitive systems are endowed with quite different properties from systems that are “brain bound” and argue that it is precisely these differences that allow human minds to transcend their biological limitations. I thus defend a complementarity version of the extended mind, according to which externally located resources and internal biological elements make a different but complementary contribution to bringing about intelligent behaviour [Sutton ]. My defence of complementarity is based on both the phylogeny and the ontogeny of cognitive systems. I initially explore the interrelation between brain and cognitive development from a neuroconstructivist perspective [Quartz & Sejnowski ; Mareshal et al. ] and then argue that our brains do not have fixed functional architectures but are sculpted and given form by the activities we repeatedly engage in. As a result of repeated engagements in socio-cultural tasks, relevant brain pathways undergo substantial rewiring. Development thus scaffolds our brains, which become geared into working in symbiotic partnership with external resources. [Kiverstein & Farina ]. On these grounds, I call into question any tendency to interpret the human biological nature as fixed and endogenously pre-determined and side with proponents of DST [Oyama ; Griffiths & Gray ] and ontogenetic niche construction [Stotz ] in arguing that we should think of natural selection as operating on whole developmental systems composed of living organisms in culturally enriched niches. [Wheeler & Clark]. Complementarity defences of EMT argue that many of the kinds of cognition humans excel at can only be accomplished by brains working together with a body that directly manipulates and acts on the world [Rowlands ; Menary ]. I take Sensory Substitution Devices as my empirical case study. SSDs exploit the remarkable plasticity of our brains and with training supply a novel perceptual modality that compensates for loss or impaired sensory channel. I argue that the coupling with these devices triggers a new mode of phenomenal access to the world, something I propose to label as a kind of “artificial synaesthesia [Ward & Meijer ].This new mode of access to the world transforms our cognitive skills and gives rise to augmented processes of deep bio-technological symbiosis. SSDs therefore become mind enhancing tools [Clark ] and a perfect case study for Complementarity. Having shown the relevance of SSDs for EMT, I then take up the possibility that these devices don’t just relocate the boundaries of cognition but may also stretch the bounds of perceptual awareness. I explore the possibility that perceivers using SSDs count as extended cognitive systems and therefore argue that the experiences they enjoy should be counted as extended conscious experiences.[Kiverstein & Farina, ]. SSDs are quite often said to involve some form of incorporation.[Clark ]. Rupert has challenged this idea and its relevance for EMT on the grounds of his embedded approach. Particularly, he has explained tool-use in terms of the causal interaction between the subject and its detached tool. In the final chapter of my dissertation I critically look at his objections and argue that all his arguments fail to apply to SSDs. In SSD perception in fact the tool becomes geared to work in symbiotic partnership with the active subject and then get factored into its’ body schema so that both of them come to form a single system of cognitive analysis. (shrink)

This paper will begin with some very broad and general considerations about the kind of biological entities we are. This exercise is motivated by the belief that the view of what we—multicellular eukaryotic organisms—are that is widely assumed by biologists, medical scientists and the general public, is an extremely limited one. It cannot be assumed a priori that a more sophisticated view will make a major difference to the science or practice of medicine, and there are areas of medicine to (...) which it is probably largely irrelevant. However, in this case there are important implications for medicine, or so I shall argue. In particular, it enables us to appreciate fully the potential medical significance of some of the most exciting contemporary advances in general biology, in such fields as epigenetics, metagenomics, and systems biology; and part of this significance is that these advances have raised serious doubts about how we should understand the biological individuals that medicine is generally assumed to aim to treat. (shrink)

The combination of evolutionary with engineering principles will enhance synthetic biology. Conversely, synthetic biology has the potential to enrich evolutionary biology by explaining why some adaptive space is empty, on Earth or elsewhere. Synthetic biology, the design and construction of artificial biological systems, substitutes bio‐engineering for evolution, which is seen as an obstacle. But because evolution has produced the complexity and diversity of life, it provides a proven toolkit of genetic materials and principles available to synthetic biology. Evolution operates on (...) the population level, with the populations composed of unique individuals that are historical entities. The source of genetic novelty includes mutation, gene regulation, sex, symbiosis, and interspecies gene transfer. At a phenotypic level, variation derives from regulatory control, replication and diversification of components, compartmentalization, sexual selection and speciation, among others. Variation is limited by physical constraints such as diffusion, and chemical constraints such as reaction rates and membrane fluidity. While some of these tools of evolution are currently in use in synthetic biology, all ought to be examined for utility. A hybrid approach of synthetic biology coupled with fine‐tuning through evolution is suggested. (shrink)

Evolutionary biology teaches that all biological complexity is the result of material mechanisms. These include principally the Darwinian mechanism of natural selection and random variation, but also include other mechanisms (symbiosis, gene transfer, genetic drift, the action of regulatory genes in development, self-organizational processes, etc.). These mechanisms are just that: mindless material mechanisms that do what they do irrespective of intelligence. To be sure, mechanisms can be programmed by an intelligence. But any such intelligent programming of evolutionary mechanisms is (...) not properly part of evolutionary biology. (shrink)