The thesis of 3D/4D equivalence states that every three-dimensional description of the world is translatable without remainder into a four-dimensional description, and vice versa. In representing an object in 3D or in 4D terms we are giving alternative descriptions of one and the same thing, and debates over whether the ontology of the physical world is "really" 3D or 4D are pointless. The twins paradox is shown to rest, in relativistic 4D geometry, on a reversed law of triangle inequality. But (...) considering the twins as 3D beings who age through time, the paradox implies that time passes at different rates in different reference frames, and therefore that the concept of a single global or Absolute time is unsustainable. (shrink)

We address the controversy in the literature concerning the definition of holobionts and the apparent constraints on their evolution using concepts from community population genetics. The genetics of holobionts, consisting of a host and diverse microbial symbionts, has been neglected in many discussions of the topic, and, where it has been discussed, a gene-centric, species-centric view, based in genomic conflict, has been predominant. Because coevolution takes place between traits or genes in two or more species and not, strictly speaking, between (...) species, it may affect some traits but not others in either host or symbiont. Moreover, when interacting species pairs are embedded in a larger community, indirect ecological effects can alter the expected pairwise dynamics. Mode of symbiont transmission and the degree of host inbreeding both affect the extent of microbial mixing across host lineages and thereby the degree to which selection on one trait of either partner affects other aspects of a holobiont phenotype. We discuss several potential defining criteria for holobionts using community genetics and population genetics models, suggesting their application and limitations. Using community genetics models, we show how conflict between genomes can be self-limiting, while cooperation and mutualism tend to be self-accelerating. It is likely that this bias in the evolutionary dynamics of interaction between hosts and symbionts is an important feature of holobionts. This bias in the evolutionary dynamic could contribute to explaining the absence of cheaters from natural mutualisms, although cheaters are predicted by gene-centered conflict theory to cause the evolutionary instability of mutualisms. Additionally, it may help explain the more frequent origin of mutualisms from parasitic than from free-living systems, an evolutionary trajectory opposite to that predicted by genome conflict theory. (shrink)

This paper explores the fundamental ideas that have motivated the idea of emergence and the movement of emergentism. The concept of reduction, which lies at the heart of the emergence idea is explicated, and it is shown how the thesis that emergent properties are irreducible gives a unified account of emergence. The paper goes on to discuss two fundamental unresolved issues for emergentism. The first is that of giving a “positive” characterization of emergence; the second is to give a coherent (...) explanation of how “downward” causation, a central component of emergentism, is able to avoid the problem of overdetermination. (shrink)

We address three fundamental questions: What does it mean for an entity to be living? What is the role of inter-organismic collaboration in evolution? What is a biological individual? Our central argument is that life arises when lineage-forming entities collaborate in metabolism. By conceiving of metabolism as a collaborative process performed by functional wholes, which are associations of a variety of lineage-forming entities, we avoid the standard tension between reproduction and metabolism in discussions of life – a tension particularly evident (...) in discussions of whether viruses are alive. Our perspective assumes no sharp distinction between life and non-life, and does not equate life exclusively with cellular or organismal status. We reach this conclusion through an analysis of the capabilities of a spectrum of biological entities, in which we include the pivotal case of viruses as well as prions, plasmids, organelles, intracellular and extracellular symbionts, unicellular and multicellular life-forms. The usual criterion for classifying many of the entities of our continuum as non-living is autonomy. This emphasis on autonomy is problematic, however, because even paradigmatic biological individuals, such as large animals, are dependent on symbiotic associations with many other organisms. These composite individuals constitute the metabolic wholes on which selection acts. Finally, our account treats cooperation and competition not as polar opposites but as points on a continuum of collaboration. We suggest that competitive relations are a transitional state, with multi-lineage metabolic wholes eventually outcompeting selfish competitors, and that this process sometimes leads to the emergence of new types or levels of wholes. Our view of life as a continuum of variably structured collaborative systems leaves open the possibility that a variety of forms of organized matter – from chemical systems to ecosystems – might be usefully understood as living entities. (shrink)

We provide an analysis of the public's having warranted epistemic trust in science, that is, the conditions under which the public may be said to have well-placed trust in the scientists as providers of information. We distinguish between basic and enhanced epistemic trust in science and provide necessary conditions for both. We then present the controversy regarding the connection between autism and measles–mumps–rubella vaccination as a case study to illustrate our analysis. The realization of warranted epistemic public trust in science (...) requires various societal conditions, which we briefly introduce in the concluding section. (shrink)

A framework for representing a specific kind of emergent property instance is given. A solution to a generalized version of the exclusion argument is then provided and it is shown that upwards and downwards causation is unproblematical for that kind of emergence. One real example of this kind of emergence is briefly described and the suggestion made that emergence may be more common than current opinions allow.

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)

That holobionts are units of selection squares poorly with the observation that microbes are often recruited from the environment, not passed down vertically from parent to offspring, as required for collective reproduction. The taxonomic makeup of a holobiont’s microbial community may vary over its lifetime and differ from that of conspecifics. In contrast, biochemical functions of the microbiota and contributions to host biology are more conserved, with taxonomically variable but functionally similar microbes recurring across generations and hosts. To save what (...) is of interest in holobiont thinking, we propose casting metabolic and developmental interaction patterns, rather than the taxa responsible for them, as units of selection. Such units need not directly reproduce or form parent-offspring lineages: their prior existence has created the conditions under which taxa with the genes necessary to carry out their steps have evolved in large numbers. These taxa or genes will reconstruct the original interaction patterns when favorable conditions occur. Interaction patterns will vary in ways that affect the likelihood of and circumstances under which such reconstruction occurs. Thus, they vary in fitness, and evolution by natural selection will occur at this level. It is on the persistence, reconstruction, and spread of such interaction patterns that students of holobiosis should concentrate, we suggest. This model also addresses other multi-species collectively beneficial interactions, such as biofilms or biogeochemical cycles maintaining all life. (shrink)

Individuality is an important concept in biology, yet there are many non-equivalent criteria of individuality expressed in different kinds of biological individuals. This article evaluates these different kinds in terms of their capacity to support explanatory generalizations over the systems they individuate. Viewing the problem of individuality from this perspective promotes a splitting strategy in which different kinds make different epistemic trade-offs that suit them for different explanatory roles. I argue that evolutionary individuals, interpreted as forming a functional kind, face (...) difficulties of individuation and explanatory power that are mitigated by relying on more structurally based properties and non-evolutionary kinds. 1Introduction2Kinds of Biological Individuals3Evolutionary Individuals and Functional Kinds4Evolutionary versus Non-evolutionary Kinds of Individuals 4.1Physiological individuality4.2Ecological individuality4.3Developmental individuality5Conclusion. (shrink)

Introduction: working together on individuality / Lynn K. Nyhart and Scott Lidgard -- The work of biological individuality: concepts and contexts / Scott Lidgard and Lynn K. Nyhart -- Cells, colonies, and clones: individuality in the volvocine algae / Matthew D. Herron -- Individuality and the control of life cycles / Beckett Sterner -- Discovering the ties that bind: cell-cell communication and the development of cell sociology / Andrew S. Reynolds -- Alternation of generations and individuality, 1851 / Lynn K. (...) Nyhart and Scott Lidgard -- Spencer's evolutionary entanglement: from liminal individuals to implicit collectivities / Snait Gissis -- Biological individuality and enkapsis: from Martin Heidenhain's synthesiology to the völkisch national community / Olivier Rieppel -- Parasitology, zoology, and society in France, ca. 1880-1920 / Michael A. Osborne -- Metabolism, autonomy, and individuality / Hannah Landecker -- Bodily parts in the structure-function dialectic / Ingo Brigandt -- Commentaries: historical, biological, and philosophical perspectives -- Distrust that particular intuition: resilient essentialisms and empirical challenges in the history of biological individuality / James Elwick -- Biological individuality: a relational reading / Scott F. Gilbert -- Philosophical dimensions of individuality / Alan C. Love and Ingo Brigandt. (shrink)

What are individuals? How can they be identified? These are crucial questions for philosophers and scientists alike. Criteria of individuality seem to differ markedly between metaphysics and the empirical sciences - and this might well explain why no work has hitherto attempted to relate the contributions of metaphysics, physics and biology on this question. This timely volume brings together various strands of research into 'individuality', examining how different sciences handle the issue, and reflecting on how this scientific work relates to (...) metaphysical concerns. The collection makes a major contribution to clarifying and overcoming obstacles to the construction of a general conception of the individual adequate for both physics and biology, and perhaps even beyond. (shrink)

Since Darwin, Biology has been framed on the idea of evolution by natural selection, which has profoundly influenced the scientific and philosophical comprehension of biological phenomena and of our place in Nature. This book argues that contemporary biology should progress towards and revolve around an even more fundamental idea, that of autonomy. Biological autonomy describes living organisms as organised systems, which are able to self-produce and self-maintain as integrated entities, to establish their own goals and norms, and to promote the (...) conditions of their existence through their interactions with the environment. Topics covered in this book include organisation and biological emergence, organisms, agency, levels of autonomy, cognition, and a look at the historical dimension of autonomy. The current development of scientific investigations on autonomous organisation calls for a theoretical and philosophical analysis. This can contribute to the elaboration of an original understanding of life - including human life - on Earth, opening new perspectives and enabling fecund interactions with other existing theories and approaches. This book takes up the challenge. (shrink)

The Limits of the Self, will be essential reading for anyone interested in the definition of biological individuality and the understanding of the immune system.

Metaphysics and Science brings together important new work within an emerging philosophical discipline: the metaphysics of science. In the opening chapter, a definition of the metaphysics of science is offered, one which explains why the topics of laws, causation, natural kinds, and emergence are at the discipline's heart. The book is then divided into four sections, which group together papers from leading academics on each of those four topics. Among the questions discussed are: How are laws and measurement methods related? (...) Can a satisfactory reductive account of laws be given? How can Lorentz transformation laws be explained? How are dispositions triggered? What role should dispositional properties play in our understanding of causation? Are natural kinds and natural properties distinct? How is the Kripke-Putnam semantics for natural kind terms related to the natural kind essentialist thesis? What would have to be the case for natural kind terms to have determinate reference? What bearing, if any, does nonlinearity in science have on the issue of metaphysical emergence? (shrink)

Our world is full of composite objects that persist through time: dogs, persons, chairs and rocks. But in virtue of what do a bunch of little objects get to compose some bigger object, and how does that bigger object persist through time? This book aims to answer these questions, but it does so by looking at accounts of composition and persistence through a new methodological lens. It asks the question: what does it take for two theories to be genuinely different, (...) and how can we know whether what seems like metaphysical disagreement is really just semantic disagreement? By offering a framework within which to explore issues of theoretical diversity, this book provides a novel way of thinking about the inter-relationship between composition and persistence. Ultimately, it argues for a new way of thinking about these issues, a way that does not preserve the standard theoretical dichotomies between four-dimensionalist theories on the one hand, and three-dimensionalist theories on the other. (shrink)

The book is an extended study of the problem of consciousness. After setting up the problem, I argue that reductive explanation of consciousness is impossible , and that if one takes consciousness seriously, one has to go beyond a strict materialist framework. In the second half of the book, I move toward a positive theory of consciousness with fundamental laws linking the physical and the experiential in a systematic way. Finally, I use the ideas and arguments developed earlier to defend (...) a form of strong artificial intelligence and to analyze some problems in the foundations of quantum mechanics. (shrink)

A systematic overview of modern metaphysics, A Survey of Metaphysics covers all of the most important topics in the field. It adopts the fairly traditional conception of metaphysics as a subject that deals with the deepest questions that can be raised concerning the fundamental structure of reality as a whole. The book is divided into six main sections that address the following themes: identity and change, necessity and essence, causation, agency and events, space and time, and universals and particulars. It (...) focuses on contemporary views and issues throughout, rather than on the history of metaphysics. (shrink)

One of our most brilliant evolutionary biologists, Richard Lewontin has also been a leading critic of those--scientists and non-scientists alike--who would misuse the science to which he has contributed so much. In The Triple Helix, Lewontin the scientist and Lewontin the critic come together to provide a concise, accessible account of what his work has taught him about biology and about its relevance to human affairs. In the process, he exposes some of the common and troubling misconceptions that misdirect and (...) stall our understanding of biology and evolution.The central message of this book is that we will never fully understand living things if we continue to think of genes, organisms, and environments as separate entities, each with its distinct role to play in the history and operation of organic processes. Here Lewontin shows that an organism is a unique consequence of both genes and environment, of both internal and external features. Rejecting the notion that genes determine the organism, which then adapts to the environment, he explains that organisms, influenced in their development by their circumstances, in turn create, modify, and choose the environment in which they live.The Triple Helix is vintage Lewontin: brilliant, eloquent, passionate, and deeply critical. But it is neither a manifesto for a radical new methodology nor a brief for a new theory. It is instead a primer on the complexity of biological processes, a reminder to all of us that living things are never as simple as they may seem. (shrink)

Motivated by the seeming structure of the sciences, metaphysical emergence combines broadly synchronic dependence coupled with some degree of ontological and causal autonomy. Reflecting the diverse, frequently incompatible interpretations of the notions of dependence and autonomy, however, accounts of emergence diverge into a bewildering variety. Here I argue that much of this apparent diversity is superficial. I first argue, by attention to the problem of higher-level causation, that two and only two strategies for addressing this problem accommodate the genuine emergence (...) of special science entities. These strategies in turn suggest two distinct schema for metaphysical emergence---'Weak' and 'Strong' emergence, respectively. Each schema imposes a condition on the powers of entities taken to be emergent: Strong emergence requires that higher-level features have more token powers than their dependence base features, whereas Weak emergence requires that higher-level features have a proper subset of the token powers of their dependence base features. Importantly, the notion of “power” at issue here is metaphysically neutral, primarily reflecting commitment just to the plausible thesis that what causes an entity may bring about are associated with how the entity is---that is, with its features. (shrink)

Individuals are a prominent part of the biological world. Although biologists and philosophers of biology draw freely on the concept of an individual in articulating both widely accepted and more controversial claims, there has been little explicit work devoted to the biological notion of an individual itself. How should we think about biological individuals? What are the roles that biological individuals play in processes such as natural selection (are genes and groups also units of selection?), speciation (are species individuals?), and (...) organismic development (do genomes code for organisms)? Much of our discussion here will focus on organisms as a central kind of biological individual, and that discussion will raise broader questions about the nature of the biological world, for example, about its complexity, its organization, and its relation to human thought. (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)

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)

This chapter introduces a distinctive approach for scientific metaphysics. Instead of drawing metaphysical conclusions by interpreting the most basic theories of science, this approach draws metaphysical conclusions by analyzing how multifaceted practices of science work. Broadening attention opens the door to drawing metaphysical conclusions from a wide range of sciences. This chapter analyzes conceptual practice in genetics to argue that the reality investigated by biologists lacks an overall structure. It expands this conclusion to motivate the no general structure thesis, which (...) states that the world lacks a general, overall structure that spans scales. It concludes that the no general structure thesis counts as metaphysics because it says something very important and general about the world. This thesis informs science as well as philosophy of science, and it provides a useful perspective for societies that look upon science to help solve complex problems in our changing world. (shrink)

All organised bodies are composed of parts, similar to those composing inorganic nature, and which have even themselves existed in an inorganic state; but the phenomena of life, which result from the juxtaposition of those parts in a certain manner, bear no analogy to any of the effects which would be produced by the action of the component substances considered as mere physical agents. To whatever degree we might imagine our knowledge of the properties of the several ingredients of a (...) living body to be extended and perfected, it is certain that no mere summing up of the separate actions of those elements will ever amount to the action of the living body itself. (shrink)

Debate about adaptationism in biology continues, in part because within “the” problem of assessing adaptationism, three distinct problems are mixed together. The three problems concern the assessment of three distinct adaptationist positions, each of which asserts the central importance of adaptation and natural selection to the study of evolution, but conceives this importance in a different way. As there are three kinds of adaptationism, there are three distinct "anti-adaptationist" positions as well. Or putting it more formally, there are three different (...) dimensions here, and strongly adaptationist views, strongly anti-adaptationist views, and moderate views are possible for each dimension. (shrink)

The nonlinearity of a composite system, whereby certain of its features (including powers and behaviors) cannot be seen as linear or other broadly additive combinations of features of the system's composing entities, has been frequently seen as a mark of metaphysical emergence, coupling the dependence of a composite system on an underlying system of composing entities with the composite system's ontological autonomy from its underlying system. But why think that nonlinearity is a mark of emergence, and moreover, of metaphysical rather (...) than merely epistemological emergence? Are there diverse ways in which nonlinearity might enter into an account of properly metaphysical emergence? And what are the prospects for there actually being phenomena that are metaphysically emergent in any available sense? Here I explore the mutual bearing of nonlinearity and metaphysical emergence, with an eye towards answering these and related questions. (shrink)

It has become customary to conceptualize the living cell as an intricate piece of machinery, different to a man-made machine only in terms of its superior complexity. This familiar understanding grounds the conviction that a cell's organization can be explained reductionistically, as well as the idea that its molecular pathways can be construed as deterministic circuits. The machine conception of the cell owes a great deal of its success to the methods traditionally used in molecular biology. However, the recent introduction (...) of novel experimental techniques capable of tracking individual molecules within cells in real time is leading to the rapid accumulation of data that are inconsistent with an engineering view of the cell. This paper examines four major domains of current research in which the challenges to the machine conception of the cell are particularly pronounced: cellular architecture, protein complexes, intracellular transport, and cellular behaviour. It argues that a new theoretical understanding of the cell is emerging from the study of these phenomena which emphasizes the dynamic, self-organizing nature of its constitution, the fluidity and plasticity of its components, and the stochasticity and non-linearity of its underlying processes. (shrink)

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)

Though most contemporary philosophers and scientists accept a physicalist view of mind, the recent surge of interest in the problem of consciousness has put the mind/body problem back into play. The physicalists' lack of success in dispelling the air of residual mystery that surrounds the question of how consciousness might be physically explained has led to a proliferation of options. Some offer alternative formulations of physicalism, but others forgo physicalism in favour of views that are more dualistic or that bring (...) in mentalistic features at the ground- floor level of reality as in pan-proto-psychism. My aim here is to give an overview of the recent philosophic discussion to serve as a map in locating issues and options. I will not offer a comprehensive survey of the debate or mark every important variant to be found in the recent literature. I will mark the principal features of the philosophic landscape that one might use as general orientation points in navigating the terrain. I will focus in particular on three central and interrelated ideas: those of emergence, reduction, and nonreductive physicalism. The third of these, which has emerged as more or less the majority view among current philosophers of mind, combines a pluralist view about the diversity of what needs to be explained by science with an underlying metaphysical commitment to the physical as the ultimate basis of all that is real. The view has been challenged from both left and right, on one side from dualists and on the other from hard core reductive materialists. Despite their differences, those critics agree in finding nonreductive physicalism an unacceptable and perhaps even incoherent position. They agree as well in treating reducibility as the essential criterion for physicality; they differ only about whether the criterion can be met. Reductive physicalists argue that it can, and dualists deny it. (shrink)

Even the simplest cell exhibits a high degree of functional differentiation (FD) realized through several mechanisms and devices contributing differently to its maintenance. Searching for the origin of FD, we briefly argue that the emergence of the respective organizational complexity cannot be the result of either natural selection (NS) or solely of the dynamics of simple self-maintaining (SM) systems. Accordingly, a highly gradual and cumulative process should have been necessary for the transition from either simple self-assembled or self-maintaining systems of (...) functionless structural components to systems with FD. We follow results of recent in vitro experiments with respect to competition among protocells, where a primitive type of selection begins to operate among them accompanied by a parallel evolution of their functional domain. We argue that minimal forms of FD should be established within the evolution of SM processes in protocells as they undergo a simpler selection process for stability and persistence in a prebiotic environment. We then suggest the concept of closure of constraints (CoC) as a way to identify and describe minimal FD in a far-from-equilibrium SM organization. We show in detail how the concept of CoC together with the conditions for its fulfillment can be applied in the case of a simple protocellular system that begins to couple internal chemical reactions with the formation of its membrane components. Finally, we discuss how such SM systems can evolve towards significantly higher levels of FD, suggesting this is mainly the result of functional recombination (formation of mechanisms) in the context of a modular SM organization. (shrink)