Given the central place organisms occupy in Kant’s account of living nature, it might seem unlikely that his claims about biological wholes could be relevant to current debates over the problem of biological individuality. These debates acknowledge the multiple realizability of biological individuality in vastly different forms, including parts of organisms and complex groups of organisms at various levels of the biological hierarchy, sparking much controversy in attempts to characterize a biological individual. I argue (...) that, far from being irrelevant to this controversy, Kant’s account provides a key insight for addressing the multiple realizability problem. I show how the reciprocal causality between a self-organizing whole and its parts, which Kant thinks characterizes a natural end, is not limited to organisms but is exhibited by numerous types of beings in living nature. Self-organizing wholes of various kinds, and at various biological levels, may count as biological individuals, depending on the degree to which their functionally integrated parts are represented by reflective judgement as a natural end. (shrink)

What are the conditions under which one biological object is a part of another biological object? This paper answers this question by developing a general, systematic account of biological parthood. I specify two criteria for biological parthood. Substantial Spatial Inclusionrequires biological parts to be spatially located inside or in the region that the natural boundary of t he biological whole occupies. Compositional Relevance captures the fact that a biological part engages in a (...) class='Hi'>biological process that must make a necessary contribution to a condition that is minimally sufficient to one or more of the characteristic behaviors of the biological whole. Instead of emphasizing the diversity of part-whole relations in the biological world, this paper asks what biological part-whole relations have in common and what constrains their existence, in general. After presenting the two criteria for biological parthood I discuss in how far my account can cope with hard cases (e.g., redundant parts) and I reveal the merits and limits of monism. (shrink)

A well-rehearsed move among teleological realists in the philosophy of biology is to base the idea of genuinely teleological forms of organic self-reproduction on a type of causality derived from Kant. Teleological realists have long argued for the causal possibility of this form of causality—in which a whole is considered the cause of its parts—as well as formulated a set of teleological criteria of adequacy for it. What is missing, to date, is an account of the mereological principles that govern (...) the envisioned whole-to-part causality. When the latter principles are taken into account, we find that there is no version of whole-to-part causality that is mereologically, causally and teleologically possible all at once, as teleological realism requires. (shrink)

Many biologists and philosophers have worried that importing models of reasoning from the physical sciences obscures our understanding of reasoning in the life sciences. In this paper we discuss one example that partially validates this concern: part-whole reductive explanations. Biology and physics tend to incorporate different models of temporality in part-whole reductive explanations. This results from differential emphases on compositional and causal facets of reductive explanations, which have not been distinguished reliably in prior philosophical analyses. Keeping these two facets distinct (...) facilitates the identifi cation of two further aspects of reductive explanation: intrinsicality and fundamentality. Our account provides resources for discriminating between different types of reductive explanation and suggests a new approach to comprehending similarities and differences in the explanatory reasoning found in biology and physics. (shrink)

This book identifies the Romantic notion of the whole as the fundamental epistemological source of the notion of structure in the thinking of the Prague Linguistic Circle, primarily its Russian representatives, and studies what amounted to the slow.

This book identifies the Romantic notion of the whole as the fundamental epistemological source of the notion of structure in the thinking of the Prague Linguistic Circle, primarily its Russian representatives, and studies what amounted to the slow.

In this essay we aim to present some considerations regarding a minimal but concrete notion of agency and goal-directed behavior that are useful for characterizing biological systems at different scales. These considerations are a particular perspective, bringing together concepts from dynamical systems, combinatorial problem-solving, and connectionist learning with an emphasis on the relationship between parts and wholes. This perspective affords some ways to think about agents that are concrete and quantifiable, and relevant to some important biological issues. (...) Instead of advocating for a strict definition of minimally agential characteristics, we focus on how (even for a modest notion of agency) the agency of a system can be more than the sum of the agency of its parts. We quantify this in terms of the problem-solving competency of a system with respect to resolution of the frustrations between its parts. This requires goal-directed behavior in the sense of delayed gratification, i.e., taking dynamical trajectories that forego short-term gains (or sustain short-term stress or frustration) in favor of long-term gains. In order for this competency to belong to the system (rather than to its parts or given by its construction or design), it can involve distributed systemic knowledge that is acquired through experience, i.e., changes in the organization of the relationships among its parts (without presupposing a system-level reward function for such changes). This conception of agency helps us think about the ways in which cells, organisms, and perhaps other biological scales, can be agential (i.e., more agential than their parts) in a quantifiable sense, without denying that the behavior of the whole depends on the behaviors of the parts in their current organization. (shrink)

Rudolf Leuckart’s 1851 pamphlet Ueber den Polymorphismus der Individuen stood at the heart of naturalists’ discussions on biological individuals, parts and wholes in mid-nineteenth-century Britain and Europe. Our analysis, which accompanies the first translation of this pamphlet into English, situates Leuckart’s contribution to these discussions in two ways. First, we present it as part of a complex conceptual knot involving not only individuality and the understanding of compound organisms, but also the alternation of generations, the division of labor (...) in nature, and the possibility of finding general laws of the organic world. Leuckart’s pamphlet is important as a novel attempt to give order to the strands of this knot. It also solved a set of key biological problems in a way that avoided some of the drawbacks of an earlier teleological tradition. Second, we situate the pamphlet within a longer trajectory of inquiry into part-whole relations in biology from the mid-eighteenth century to the present. We argue that biological individuality, along with the problem-complexes with which it engaged, was as central a problem to naturalists before 1859 as evolution, and that Leuckart’s contributions to it left a long legacy that persisted well into the twentieth century. As biologists’ interests in part-whole relations are once again on the upswing, the longue durée of this problem merits renewed consideration. (shrink)

Rudolf Leuckart's 1851 pamphlet Ueber den Polymorphismus der Individuen (On the polymorphism of individuals) stood at the heart of naturalists' discussions on biological individuals, parts and wholes in mid-nineteenth-century Britain and Europe. Our analysis, which accompanies the first translation of this pamphlet into English, situates Leuckart's contribution to these discussions in two ways. First, we present it as part of a complex conceptual knot involving not only individuality and the understanding of compound organisms, but also the alternation of (...) generations, the division of labor in nature, and the possibility of finding general laws of the organic world. Leuckart's pamphlet is important as a novel attempt to give order to the strands of this knot. It also solved a set of key biological problems in a way that avoided some of the drawbacks of an earlier teleological tradition. Second, we situate the pamphlet within a longer trajectory of inquiry into part-whole relations in biology from the mid-eighteenth century to the present. We argue that biological individuality, along with the problem-complexes with which it engaged, was as central a problem to naturalists before 1859 as evolution, and that Leuckart's contributions to it left a long legacy that persisted well into the twentieth century. As biologists' interests in part-whole relations are once again on the upswing, the longue durée of this problem merits renewed consideration. (shrink)

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

Whole Brain Emulation has been championed as the most promising, well-defined route to achieving both human-level artificial intelligence and superintelligence. It has even been touted as a viable route to achieving immortality through brain uploading. WBE is not a fringe theory: the doctrine of Computationalism in philosophy of mind lends credence to the in-principle feasibility of the idea, and the standing of the Human Connectome Project makes it appear to be feasible in practice. Computationalism is a popular, independently plausible theory, (...) and Connectomics a well-funded empirical research program, so optimism about WBE is understandable. However, this optimism may be misplaced. This article argues that WBE is, at best, no more compelling than any of the other far-flung routes to achieving superintelligence. Similarly skeptical conclusions are found regarding immortality. The essay concludes with some positive considerations in favor of the Biological Theory of consciousness, as well as morals about the limits of Computationalism in both artificial intelligence and the philosophy of mind more generally. (shrink)

This book provides a comprehensive guide to the conceptual methodological, and epistemological problems of biology, and treats in depth the major developments in molecular biology and evolutionary theory that have transformed both biology and its philosophy in recent decades. At the same time the work is a sustained argument for a particular philosophy of biology that unifies disparate issues and offers a framework for expectations about the future directions of the life sciences. The argument explores differences between autonomist and anti-autonomist (...) views of biology. The result is a vindication of reductionism, but one that is unexpectedly hollow. For it leaves the exponents of the autonomy of biology from physical science with as much as their view of biology really requires - and rather more than the reductionist might comfortably concede. Professor Rosenberg shows how the problems of the philosophy of biology are interconnected and how their solutions are interdependent, However, this book focuses more on the direct concerns of biologists, rather than the traditional agenda of philosophers' problems about biology. This departure from earlier books on the subject results both in greater understanding and relevance of the philosophy of science to biology as a whole. (shrink)

A scientific explanatory project, part-whole explanation, and a kind of science, part-whole science are premised on identifying, investigating, and using parts and wholes. In the biological sciences, mechanistic, structuralist, and historical explanations are part-whole explanations. Each expresses different norms, explananda, and aims. Each is associated with a distinct partitioning frame for abstracting kinds of parts. These three explanatory projects can be complemented in order to provide an integrative vision of the whole system, as is shown for a detailed (...) case study: the tetrapod limb. My diagnosis of part-whole explanation in the biological sciences as well as in other domains exploring evolved, complex, and integrated systems (e.g., psychology and cognitive science) cross-cuts standard philosophical categories of explanation: causal explanation and explanation as unification. Part-whole explanation is itself one essential aspect of part-whole science. (shrink)

There is a limited understanding amongst scientists, students and the public about realizing trust in scientific findings. This should be a paramount objective, or is it only about career ambition? What is the role of the individual? Scientists and the public need to know more about the link between the philosophy of science and the science research methods. There is a limited understanding of why accuracy is important and that it is not the same as precision. Also, there is often (...) the need to measure an approximation of a real system and the classic case is reductionism in biology versus whole organism biology. The author brings these topics together in terms of trusting in science. (shrink)

The chronologic age classically used in demography is often unable to give useful information about which exact stage in development or aging processes has reached an organism. Hence, we propose here to explain in some applications for what reason the chronologic age fails in explaining totally the observed state of an organism, which leads to propose a new notion, the biological age. This biological age is essentially determined by the number of divisions before the Hayflick’s limit the tissue (...) or mitochondrion in a critical organ (in the sense where its loss causes the death of the whole organism) has already used for its development and adult phases. We give a precise definition of the biological age of an organ based on the Hayflick’s limit of its cells and we introduce a desynchronization index (the cell entropy) for some critical tissues or membranes, which are mainly skin, intestinal endothelium, alveoli epithelium and mitochondrial inner membrane. In these actively metabolising interface tissues or membranes, there is a rapid turnover of cells, of their cytoplasmic constituents such as proteins, and of membrane lipids. The boundaries corresponding to these tissues, cells or membranes have vital functions of interface with the environment (protection, homeothermy, nutrition and respiration) and have a rapid turnover (the total cell renewal time is in mice equal to 3 weeks for the skin, 1.5 day for the intestine, 4 months for the alveolae and 11 days for mitochondrial inner membrane) conditioning their biological age. The biological age of a tissue is made of two major components: (1) first, its embryonic age based on the distance (in number of divisions) between the birth date of its first differentiated cell and the time until it reaches its final boundary at the end of its development and (2) second, its adult age whose complement until its death is just the lapse of time made of the sum of remaining cell cycle durations authorized by its Hayflick’s limit. From this definition, we calculate the global biological lifespan of an organism and revisit notions like demographic survival curves, duration and synchrony of cell cycles, living boundaries from proto-cells to organs, and embryonic and adult phases duration. (shrink)

This short and highly accessible volume opens up the subject of the philosophy of biology to professionals and to students in both disciplines. The text covers briefly and clearly all of the pertinent topics in the subject, dealing with both human and non-human issues, and quite uniquely surveying not only scholars in the English-speaking world but others elsewhere, including the Eastern block. As molecular biologists peer ever more deeply into life’s mysteries, there are those who fear that such ‘reductionism’ conceals (...) more than it reveals, and there are those who complain that the new techniques threaten the physical safety of us all. As students of evolution apply their new-found understanding to our own species, some people think that this is merely an excuse for racist and sexist propaganda, and others worry that the whole exercise blatantly violates the religious beliefs many of us hold dear. These controversies are the joint concern of biologists and philosophers—of those whose task it is to study the theoretical and moral foundations of knowledge. The comprehensive and fully up-to-date bibliography makes this an invaluable and indispensable guide. (shrink)

Whole brain emulation aims to re-implement functions of a mind in another computational substrate with the precision needed to predict the natural development of active states in as much as the influence of random processes allows. Furthermore, brain emulation does not present a possible model of a function, but rather presents the actual implementation of that function, based on the details of the circuitry of a specific brain. We introduce a notation for the representations of mind state, mind transition functions (...) and transition update functions, for which elements and their relations must be quantified in accordance with measurements in the biological substrate. To discover the limits of significance in terms of the temporal and spatial resolution of measurements, we point out the importance of brain region and task specific constraints, as well as the importance of in-vivo measurements. We summarize further problems that need to be addressed. (shrink)

The mechanistic perspective has dominated biological disciplines such as biochemistry, physiology, cell and molecular biology, and neuroscience, especially during the 20th century. The primary strategy is reductionist: organisms are to be decomposed into component parts and operations at multiple levels. Researchers adopting this perspective have generated an enormous body of information about the mechanisms of life at scales ranging from the whole organism down to genetic and other molecular operations.

Aristotle's biological works - constituting over 25% of his surviving corpus and for centuries largely unstudied by philosophically oriented scholars - have been the subject of an increasing amount of attention of late. This collection brings together some of the best work that has been done in this area, with the aim of exhibiting the contribution that close study of these treatises can make to the understanding of Aristotle's philosophy. The book is divided into four parts, each with an (...) introduction which places its essays in relation to each other and to the wider issues of the book as a whole. The first part is an overview of the relationship of Aristotle's biology to his philosophy; the other three each concentrate on a set of issues central to Aristotelian study - definition and demonstration; teleology and necessity in nature; and metaph themes such as the unity of matter and form and the nature of substance. (shrink)

The new mechanists and the autonomy approach both aim to account for how biological phenomena are explained. One identifies appeals to how components of a mechanism are organized so that their activities produce a phenomenon. The other directs attention towards the whole organism and focuses on how it achieves self-maintenance. This paper discusses challenges each confronts and how each could benefit from collaboration with the other: the new mechanistic framework can gain by taking into account what happens outside individual (...) mechanisms, while the autonomy approach can ground itself in biological research into how the actual components constituting an autonomous system interact and contribute in different ways to realize and maintain the system. To press the case that these two traditions should be constructively integrated we describe how three recent developments in the autonomy tradition together provide a bridge between the two traditions: (1) a framework of work and constraints, (2) a conception of function grounded in the organization of an autonomous system, and (3) a focus on control. (shrink)

Synthetic biology is a dynamic, young, ambitious, attractive, and heterogeneous scientific discipline. It is constantly developing and changing, which makes societal evaluation of this emerging new science a challenging task, prone to misunderstandings. Synthetic biology is difficult to capture, and confusion arises not only regarding which part of synthetic biology the discussion is about, but also with respect to the underlying concepts in use. This book offers a useful toolbox to approach this complex and fragmented field. It provides a (...) class='Hi'>biological access to the discussion using a 'layer' model that describes the connectivity of synthetic or semisynthetic organisms and cells to the realm of natural organisms derived by evolution. Instead of directly reviewing the field as a whole, firstly our book addresses the characteristic features of synthetic biology that are relevant to the societal discussion. Some of these features apply only to parts of synthetic biology, whereas others are relevant to synthetic biology as a whole. In the next step, these new features are evaluated with respect to the different areas of synthetic biology. Do we have the right words and categories to talk about these new features? In the third step, traditional concepts like "life" and "artificiality" are scrutinized with regard to their discriminatory power. This approach may help to differentiate the discussion on synthetic biology. Lastly our refined view is utilized for societal evaluation. We have investigated the public views and attitudes to synthetic biology. It also includes the analysis of ethical, risk and legal questions, posed by present and future practices of synthetic biology. This book contains the results of an interdisciplinary research project and presents the authors' main findings and recommendations. They are addressed to science, industry, politics and the general public interested in this upcoming field of biotechnology. (shrink)

The schematic concept of levels of causal interaction is applied to the relation between genetics and biology. The strength of classical formal genetics lies in its power to proceed directly from observations on an external phenotype, to inferences concerning the nature and properties of the fundamental genetic factors. Its weakness comes from the fact that by short-circuiting the causal chain leading from genotype to phenotype, it creates a divorce between genetics and biology. It is argued that in order to reestablish (...) an articulation of genetics and the biology of whole organisms, it will be necessary to study in detail the entire causal chain leading from a difference in a genetic factor to a difference in a corresponding phenotypic character. This proposal is illustrated by a consideration of multifactorial diseases, which appear to be due to strong interactions between a moderate number of distinct loci; the frequency of abnormal alleles at any given locus may be surprisingly high. (shrink)

Whole brain emulation aims to re-implement functions of a mind in another computational substrate with the precision needed to predict the natural development of active states in as much as the influence of random processes allows. Furthermore, brain emulation does not present a possible model of a function, but rather presents the actual implementation of that function, based on the details of the circuitry of a specific brain. We introduce a notation for the representations of mind state, mind transition functions (...) and transition update functions, for which elements and their relations must be quantified in accordance with measurements in the biological substrate. To discover the limits of significance in terms of the temporal and spatial resolution of measurements, we point out the importance of brain region and task specific constraints, as well as the importance of in-vivo measurements. We summarize further problems that need to be addressed. (shrink)

T he term emergence is used to describe the appearance of new properties that arise when a system exceeds a certain level of size or complexity, properties that are absent from the constituents of the system. It is a concept often summed up by the phrase that “the whole is greater than the sum of its parts,” and it is a key notion in the burgeoning field of complexity science. Life is often cited as a classic example of an emergent (...) phenomenon: no atoms of my body are living, yet I am living (see, for example, Morowitz [1]). Biological organisms depend on the processes of their constituent parts, yet they nevertheless exhibit a degree of autonomy from their parts (see, for example, Kauffman [2]). How can this be? These seem to be contradictory properties. (shrink)

In this book, the author defends the substantial unity of a human person whose life endures through time. Because a human being is an irreducible whole (including biological, psychological, and narrative powers), our lives can have personal coherence over time. The whole temporal expanse of a life is prior to any of its stages, just as a whole human person is prior to any of her organs or powers. We can tell stories about our past, present, and future only (...) because we possess a certain kind of complex unity at any one time. What we are as human beings makes it possible for us to lead the life of a human person. (shrink)

This paper has two parts: In the first part, I give a general survey of the various reasons 17th and 18th century life scientists and metaphysicians endorsed the theory of pre-existence according to which God created all living beings at the creation of the universe, and no living beings are ever naturally generated anew. These reasons generally fall into three categories. The first category is theological. For example, many had the desire to account for how all humans are stained by (...) original sin (we were all there). As another example of a theological motivation, some take the organism as an obvious starting point for a teleological argument for God’s existence, and this staring point is sometimes developed into a full-blown theory of pre-existence. The second category could be thought of as non-theological metaphysical, and paramount here is the desire to deal with the metaphysical problem of individuation. So, for example, Leibniz embraces a version of hylomorphism in order to overcome difficulties with Descartes’ theory of material substance, including the difficulty of how to account for enduring material individuals, and Leibniz’s hylomorphism is closely linked with his embrace of pre-existence. The third category might be termed “biological”, and one example of such a concern is how to explain the organic unity of living beings where the whole seems to ontologically precede the parts. This is frequently translated into a temporal priority of whole to parts, and thus pre-existence is posited. Of course, many natural philosophers of the early modern period embrace pre-existence for more than one reason, but in general, these are the three classes of motivations one might have for embracing the theory. In the second part of the paper I examine in detail one argument that appears in the work of Malebranche. On the face of it, this argument seems to be a biological one, specifically the biological or organic holism argument mentioned above. But upon closer examination, I shall argue, Malebranche’s reasons for endorsing pre-existence bring together several of the arguments discussed in the first part of the paper. I conclude with some considerations about what we can learn about Malebranche as a natural philosopher from his motivations for holding the pre-existence doctrine of generation. (shrink)

This chapter examines five emulation methods, drawing a distinction between structure replication and reconstruction (SR) methods, and reverse brain engineering (RBE) methods. It argues that we need reasons to claim a particular procedure does or does not maintain identity, independently of whether the procedure is destructive or nondestructive. The chapter proposes that whole brain emulation (WBE) research be aimed primarily at cybernetics and possibility of replacing a biological brain in steps that involve very small parts with no psychologically relevant (...) structure. It also argues that methods reliant on structure replication and reconstruction will not preserve personal identity, based on a neo‐Lockean definition of personal identity according to which the self is a relatively autonomous self‐perpetuating substance whose psychological continuity through time is ensured primarily by immanent causation. All SR methods involve too much transeunt causation. (shrink)

Based on a conference on the nature and origin of biological information held at Cornell University in 2011, this edited volume presents new research by experts in information theory, computer science, numerical simulation, thermodynamics, evolutionary theory, whole organism biology, developmental biology, molecular biology, genetics, physics, biophysics, mathematics, and linguistics.

Biological boundaries are important because of what they reveal about the evolution of a lineage, the relationship between organisms of different lineages, the structure and function of particular subsystems of the organism, the interconnection between an organism and its environment, and a myriad of other important issues related to individuality, development, and evolution. Since there is no single unifying theory for all biological sciences, there are various possible theoretical characterizations of what counts as a biological boundary. Theoretical (...) specificity is crucial for the full characterization of a boundary; to this end, it is useful to begin with general properties and then to compare these to those properties specific to a particular biological boundary. This dual heuristic approach—top-down and bottom-up—can then be repeated to increase the robustness of the boundary characterization. In what follows, I explore both the general structural and functional aspects of biological boundaries and those specific to a biological subsystem, which itself is critical to boundary formation, maintenance, and evolution—the vertebrate immune system. It is a remarkable and sobering regularity of nature that organisms remain whole because their parts are constantly being built up and broken down, and this is no less true of their boundaries. The vertebrate immune system is at the center of this process of biological boundary maintenance and breakdown. (shrink)

Philosophers have traditionally assumed that the difference between active and passive movement could be explained by the presence or absence of an intention in the mind of the agent. This assumption has led to the neglect of many interesting active behaviors that do not depend on intentions, including the "mindless" actions of humans and the activities of non-human animals. In this book Jones offers a broad account of agency that unifies these cases. The book addresses a range of questions, including: (...) When are movements properly attributed to whole agents, rather than to their parts? What does it mean for an agent to guide its action? What distinguishes agents from other complex systems? What is the relationship between action and adaptive behavior? And why might the study of living systems be the key to understanding agency? This book makes an important contribution to current philosophical debate on the nature and origins of agency. It defines action as a uniquely biological process and recasts human intentional action as a specialized case of a broader and more common phenomenon than has been previously assumed. Uniting findings from philosophy, cognitive science, psychology, biology, computer science, complexity theory and ethology, this book will be of interest to students and scholars working in these areas. (shrink)

As is clear in the 2008 report of the President's Council on Bioethics, the brain death debate is plagued by ambiguity in the use of such key terms as ‘integration’ and ‘wholeness’. Addressing this problem, I offer a plausible ontological account of organismal unity drawing on the work of Hoffman and Rosenkrantz, and then apply that account to the case of brain death, concluding that a brain dead body lacks the unity proper to a human organism, and has therefore undergone (...) a substantial change. I also show how my view can explain hard cases better than one in which biological integration is taken to imply ontological wholeness or unity. (shrink)

Michael Ghiselin and David Hull’s individuality thesis is that biological species are individuals. Philosophers often treat the term “individual” as synonymous with “mereological sum” and characterize it in terms of mereology. It is easy to see how the biological project has been interpreted as a mereological one. This chapter argues that this is a mistake, that biological part/whole relations often violate the axioms of mereology. Conflating these projects confuses the central issues at stake in both, and makes (...) the job of evaluating either unnecessarily burdensome. Clarifying this helps identify the genuine metaphysical implications of the individuality thesis, which serves as an exemplar of scientifically informed metaphysics. (shrink)

Reconstructability analysis (RA) decomposes wholes, namely data in the form either of set theoretic relations or multivariate probability distributions, into parts, namely relations or distributions involving subsets of variables. Data is modeled and compressed by variable-based decomposition, by more general state-based decomposition, or by the use of latent variables. Models, which specify the interdependencies among the variables, are selected to minimize error and complexity.

The foundations of systematics lie in ontology, not in subjective epistemology. Systems and their elements should be distinguished from classes; only the latter are constructed from similarities. The term classification should be restricted to ordering into classes; ordering according to systematic relations may be called systematization.The theory of organization levels portrays the real world as a hierarchy of open systems, from energy quanta to ecosystems; followingHartmann these systems as extended in time are considered the primary units of reality. Organization levels (...) should be distinguished from levels of differentiation within each organization level.Certain biological systems, such as species, continue to be misinterpreted as classes, particularly by logicians unfamiliar with modern biological theory. Replacement of Aristotelian definitions of species by “polytypic” definitions achieves nothing, because species are individual systems which can be defined from an ontological viewpoint only as wholes. The dispute whether classes are real per se or only in individuals is of no scientific importance; irrespective of which view is taken, any ordering of physical objects into classes constitutes an hypothesis about the structure of the real world.The distinction between essential and contingent characters is relevant only to classification. There are no universal rules for evaluating characters for purposes of systematization. Character statements do not form separate linear sequences. The search for “unit characters” in an absolute sense is futile. All real characters are reducible to relations and are in principle measurable, although there are limitations on the extent to which this can be presently achieved.The concept of the sexual species is fundamental to theories of biosystematics. Sexual species may be defined as lineages consisting at any given time of series of populations between which genetic exchange can occur and delimited in time by two successive processes of speciation. Linnaean nomenclature needs modification; in its traditional form it is appropriate only to non-truncated hierarchies, whereas real phylogenies form truncated hierarchies. In consequence of the distinction between systematization and classification it is concluded that, while taxa may be classified into age classes or evolutionary grades, their limits as taxa can be no different in either case. Classification into evolutionary grades remains an imprecise endeavour, since no general measure of evolutionary differentiation has been devised.The spatial and temporal extent of ecosystems, the postulated basic units of ecosystematics, remains unclarified. Nevertheless there are grounds for expecting progress in this field as the energetic relations between organisms become better understood. Biotic communities are not “abstract” classes, but systematic units. Physiognomic classification should not be confused with systematization of plant communities; both approaches contribute to an understanding of vegetational structure. (shrink)

A physiological function can be described as a cycle based on a cusp bifurcation set in catastrophe theory. This cycle involves four phases that are successively developed along a functional potential, which is used to perform a given physiological act. The work we present is firstly based on a detailed study of the global function of vision, which covers a vast field extending from the molecular to cerebral scale. We then present other examples of generalised functions by expanding the frame (...) of reference, from the scale of an organ to the scale of a whole organism with predation function, and to the scale of a social group with crisis management. We observed that the criteria remain the same, whether the function is considered on the scale of a cell membrane or a group of individuals organised into a cohort. Moreover, a so-called generalised function can be broken down into simpler sub-functions, each phase of the initial function containing the physiological act of each sub-function. It seems thus that a fractal extension may characterise the four-cusp spiral. This spiral is increasingly large as the types of sub-functions are multiplied. In functions relative to sociological science, such as crisis management, which are not natural but built and designed by humans, close attention must be paid to following the rules of these generalised biological functions. (shrink)

There are two fundamentally distinct kinds of biological theorizing. "Formal biology" focuses on the relations, captured in formal laws, among mathematically abstracted properties of abstract objects. Population genetics and theoretical mathematical ecology, which are cases of formal biology, thus share methods and goals with theoretical physics. "Compositional biology," on the other hand, is concerned with articulating the concrete structure, mechanisms, and function, through developmental and evolutionary time, of material parts and wholes. Molecular genetics, biochemistry, developmental biology, and physiology, (...) which are examples of compositional biology, are in serious need of philosophical attention. For example, the very concept of a "part" is understudied in both philosophy of biology and philosophy of science. ;My dissertation is an attempt to clarify the distinction between formal biology and compositional biology and, in so doing, provide a clear philosophical analysis, with case studies, of compositional biology. Given the social, economic, and medical importance of compositional biology, understanding it is urgent. For my investigation, I draw on the philosophical fields of metaphysics and epistemology, as well as philosophy of biology and philosophy of science. I suggest new ways of thinking about some classic philosophy of science issues, such as modeling, laws of nature, abstraction, explanation, and confirmation. I hint at the relevance of my study of two kinds of biological theorizing to debates concerning the disunity of science. (shrink)

The idea of organism, which of recent years has bulked so largely in scientific, and especially in biological, theory has been developed mainly in reference to living organisms, and has been extended to cover such systems as human societies, crystals, molecules and atoms—and indeed the whole universe has been interpreted as an organism. This use of the term, however, includes different ways in which parts may be together in a system. The belief that the principle of organism has been (...) wrongly extended to explain certain co-ordinations of vital processes which require a different type of explanation is the reason for this addition to the immense literature on the subject of organism. (shrink)

Simulation and Similarity: Using Models to Understand the World is an account of modeling in contemporary science. Modeling is a form of surrogate reasoning where target systems in the natural world are studied using models, which are similar to these targets. My book develops an account of the nature of models, the practice of modeling, and the similarity relation that holds between models and their targets. I also analyze the conceptual tools that allow theorists to identify the trustworthy aspects of (...) models. Taken as a whole, I try to account for the ways that modeling is actually practiced by theorists, while abstracting sufficiently to understand the similarities and differences among examples of concrete, mathematical, and computational modeling.I am grateful to Wendy Parker, Jay Odenbaugh, and Bill Wimsatt for their careful and interesting reading of my book, as well as their constructive criticisms. Although I naturally disagree with some of their critiques, I have learned much .. (shrink)

Kant's Critique of Judgment has often been interpreted by scholars as comprising separate treatments of three uneasily connected topics: beauty, biology, and empirical knowledge. Rachel Zuckert's book interprets the Critique as a unified argument concerning all three domains. She argues that on Kant's view, human beings demonstrate a distinctive cognitive ability in appreciating beauty and understanding organic life: an ability to anticipate a whole that we do not completely understand according to preconceived categories. This ability is necessary, moreover, for human (...) beings to gain knowledge of nature in its empirical character as it is, not as we might assume it to be. Her wide-ranging and original study will be valuable for readers in all areas of Kant's philosophy. (shrink)

Evolutionary developmental biology (evo-devo) is considered a ‘mechanistic science,’ in that it causally explains morphological evolution in terms of changes in developmental mechanisms. Evo-devo is also an interdisciplinary and integrative approach, as its explanations use contributions from many fields and pertain to different levels of organismal organization. Philosophical accounts of mechanistic explanation are currently highly prominent, and have been particularly able to capture the integrative nature of multifield and multilevel explanations. However, I argue that evo-devo demonstrates the need for a (...) broadened philosophical conception of mechanisms and mechanistic explanation. Mechanistic explanation (in terms of the qualitative interactions of the structural parts of a whole) has been developed as an alternative to the traditional idea of explanation as derivation from laws or quantitative principles. Against the picture promoted by Carl Craver, that mathematical models describe but usually do not explain, my discussion of cases from the strand of evo-devo which is concerned with developmental processes points to qualitative phenomena where quantitative mathematical models are an indispensable part of the explanation. While philosophical accounts have focused on the actual organization and operation of mechanisms, properties of developmental mechanisms that are about how a mechanism reacts to modifications are of major evolutionary significance, including robustness, phenotypic plasticity, and modularity. A philosophical conception of mechanisms is needed that takes into account quantitative changes, transient entities and the generation of novel types of entities, feedback loops and complex interaction networks, emergent properties, and, in particular, functional-dynamical aspects of mechanisms, including functional (as opposed to structural) organization and distributed, system-wide phenomena. I conclude with general remarks on philosophical accounts of explanation. (shrink)

Alan Shewmons article, The brain and somatic integration: Insights into the standard biological rationale for equating brain death with death (2001), strikes at the heart of the standard justification for whole brain death criteria. The standard justification, which I call the standard paradigm, holds that the permanent loss of the functions of the entire brain marks the end of the integrative unity of the body. In my response to Shewmons article, I first offer a brief summary of the standard (...) paradigm and cite recent work by advocates of whole brain criteria who tenaciously cling to the standard paradigm despite increasing evidence showing that it has significant weaknesses. Second, I address Shewmons case against the standard paradigm, arguing that he is successful in showing that whole brain dead patients have integrated organic unity. Finally, I discuss some minor problems with Shewmons article, along with suggestions for further elaboration. (shrink)

I go deep into the biology of the human organism to argue that the psychological features and functions of persons are realized by cellular and molecular parallel distributed processing networks dispersed throughout the whole body. Persons supervene on the computational processes of nervous, endocrine, immune, and genetic networks. Persons do not go with brains.

The metaphorical nature of biological language is examined and the use of metaphors for providing the linguistic context in which similarities and differences are made is described. Certain pervasive metaphors which are characterised by systemic properties are noted, and in order to provide some focus to the study, systemic metaphors associated with machine, text and organism are discussed. Other systemic metaphors such as society and circuit are also reported. Some details concerning interrelations between automaton and organism are presented in (...) the light of the previous discussion.An approach towards the analysis of biosystem metaphors is outlined which relates part-whole, organisational level and systemic metaphors in a single model. Examples are provided throughout the discussion and mainly come from computing. The potential for metaphorical transfers between these domains is considered. (shrink)

Unlike in physics, the category of thought experiment is not very common in biology. At least there are no classic examples that are as important and as well-known as the most famous thought experiments in physics, such as Galileo’s, Maxwell’s or Einstein’s. The reasons for this are far from obvious; maybe it has to do with the fact that modern biology for the most part sees itself as a thoroughly empirical discipline that engages either in real natural history or in (...) experimenting on real organisms rather than fictive ones. While theoretical biology does exist and is recognized as part of biology, its role within biology appears to be more marginal than the role of theoretical physics within physics. It could be that this marginality of theory also affects thought experiments as sources of theoretical knowledge. Of course, none of this provides a sufficient reason for thinking that thought experiments are really unimportant in biology. It is quite possible that the common perception of this matter is wrong and that there are important theoretical considerations in biology, past or present, that deserve the title of thought experiment just as much as the standard examples from physics. Some such considerations may even be widely known and considered to be important, but were not recognized as thought experiments. In fact, as we shall see, there are reasons for thinking that what is arguably the single most important biological work ever, Charles Darwin’s On the Origin of Species, contains a number of thought experiments. There are also more recent examples both in evolutionary and non-evolutionary biology, as we will show. Part of the problem in identifying positive examples in the history of biology is the lack of agreement as to what exactly a thought experiment is. Even worse, there may not be more than a family resemblance that unifies this epistemic category. We take it that classical thought experiments show the following characteristics: They serve directly or indirectly in the non-empirical epistemic evaluation of theoretical propositions, explanations or hypotheses. Thought experiments somehow appeal to the imagination. They involve hypothetical scenarios, which may or may not be fictive. In other words, thought experiments suppose that certain states of affairs hold and then try to intuit what would happen in a world where these suppositions are true. We want to examine in the following sections if there are episodes in the history of biology that satisfy these criteria. As we will show, there are a few episodes that might satisfy all three of these criteria, and many more if the imagination criterion is dropped or understood in a lose sense. In any case, this criterion is somewhat vague in the first place, unless a specific account of the imagination is presupposed. There will also be issues as to what exactly “non-empirical” means. In general, for the sake of discussion we propose to understand the term “thought experiment” here in a broad rather than a narrow sense here. We would rather be guilty of having too wide a conception of thought experiment than of missing a whole range of really interesting examples. (shrink)

Synthetic biology is often understood in terms of the pursuit for well-characterized biological parts to create synthetic wholes. Accordingly, it has typically been conceived of as an engineering dominated and application oriented field. We argue that the relationship of synthetic biology to engineering is far more nuanced than that and involves a sophisticated epistemic dimension, as shown by the recent practice of synthetic modeling. Synthetic models are engineered genetic networks that are implanted in a natural cell environment. Their (...) construction is typically combined with experiments on model organisms as well as mathematical modeling and simulation. What is especially interesting about this combinational modeling practice is that, apart from greater integration between these different epistemic activities, it has also led to the questioning of some central assumptions and notions on which synthetic biology is based. As a result synthetic biology is in the process of becoming more “biology inspired.”. (shrink)

As innovations in the field of vascular composite allotransplantation (VCA) progress, whole-eye transplantation (WET) is poised to transition from non-human mammalian models to living human recipients. Present treatment options for vision loss are generally considered suboptimal, and attendant concerns ranging from aesthetics and prosthesis maintenance to social stigma may be mitigated by WET. Potential benefits to WET recipients may also include partial vision restoration, psychosocial benefits related to identity and social integration, improvements in physical comfort and function, and reduced surgical (...) risk associated with a biologic eye compared to a prosthesis. Perioperative and postoperative risks of WET are expected to be comparable to those of facial transplantation (FT), and may be similarly mitigated by immunosuppressive protocols, adequate psychosocial support, and a thorough selection process for both the recipient and donor. To minimize the risks associated with immunosuppressive medications, the first attempts in human recipients will likely be performed in conjunction with a FT. If first-in-human attempts at combined FT-WET prove successful and the biologic eye survives, this opens the door for further advancement in the field of vision restoration by means of a viable surgical option. This analysis integrates recent innovations in WET research with the existing discourse on the ethics of surgical innovation and offers preliminary guidance to VCA programs considering undertaking WET in human recipients. (shrink)

Back cover: This book develops a philosophical account that reveals the major characteristics that make an explanation in the life sciences reductive and distinguish them from non-reductive explanations. Understanding what reductive explanations are enables one to assess the conditions under which reductive explanations are adequate and thus enhances debates about explanatory reductionism. The account of reductive explanation presented in this book has three major characteristics. First, it emerges from a critical reconstruction of the explanatory practice of the life sciences itself. (...) Second, the account is monistic since it specifies one set of criteria that apply to explanations in the life sciences in general. Finally, the account is ontic in that it traces the reductivity of an explanation back to certain relations that exist between objects in the world (such as part-whole relations and level relations), rather than to the logical relations between sentences. Beginning with a disclosure of the meta-philosophical assumptions that underlie the author’s analysis of reductive explanation, the book leads into the debate about reduction(ism) in the philosophy of biology and continues with a discussion on the two perspectives on explanatory reduction that have been proposed in the philosophy of biology so far. The author scrutinizes how the issue of reduction becomes entangled with explanation and analyzes two concepts, the concept of a biological part and the concept of a level of organization. The results of these five chapters constitute the ground on which the author bases her final chapter, developing her ontic account of reductive explanation. (shrink)