Among the notions of levels invoked in accounts of biological phenomena, I focus on two: levels of production mechanisms and levels of control mechanisms. I argue that these two notions of level exhibit different characteristics: production mechanisms are organized hierarchically while control mechanisms are often organized heterarchically. I illustrate the differences in these modes of organization by examining production and control mechanisms involved in cell division in Escherichia coli and in circulation of blood in mammals. I conclude by exploring (...) how these two notions of levels can be integrated by adopting a perspective in which organisms are autonomous systems maintaining themselves far from equilibrium. (shrink)

Living organisms act as integrated wholes to maintain themselves. Individual actions can each be explained by characterizing the mechanisms that perform the activity. But these alone do not explain how various activities are coordinated and performed versatilely. We argue that this depends on a specific type of mechanism, a control mechanism. We develop an account of control by examining several extensively studied control mechanisms operative in the bacterium E. coli. On our analysis, what distinguishes a control mechanism from other (...) mechanisms is that it relies on measuring one or more variables, which results in setting constraints in the control mechanism that determine its action on flexible constraints in other mechanisms. In the most basic arrangement, the measurement process directly determines the action of the control mechanism, but in more complex arrangements signals mediate between measurements and effectors. This opens the possibility of multiple responses to the same measurement and responses based on multiple measurements. It also allows crosstalk, resulting in networks of control mechanisms. Such networks integrate the behaviors of the organism but also present a challenge in tailoring responses to particular measurements. We discuss how integrated activity can still result in differential, versatile, responses. (shrink)

Aristotle uses two kinds of material cause in his analysis of biological organisms: compositional matter, which persists through their birth and death;and functional matter, which consists of the organs and functional parts out of which biological organisms are made while they are alive. These two kinds of material cause, it has been argued, have quite different explanatory roles: functional matter is required by biological organisms to perform their essential functions,but compositional matter contributes nothing necessary (...) to them and is only responsible for their accidental properties. Against this view, I argue that biological organisms are systematically dependent upon their compositional matter and the latter is responsible for many of their necessary attributes. (shrink)

The genetic code appeared on Earth with the first cells. The codes of cultural evolution arrived almost four billion years later. These are the only codes that are recognized by modern biology. In this book, however, Marcello Barbieri explains that there are many more organic codes in nature, and their appearance not only took place throughout the history of life but marked the major steps of that history. A code establishes a correspondence between two independent 'worlds', and the codemaker is (...) a third party between those 'worlds'. Therefore the cell can be thought of as a trinity of genotype, phenotype and ribotype. The ancestral ribotypes were the agents which gave rise to the first cells. The book goes on to explain how organic codes and organic memories can be used to shed new light on the problems encountered in cell signalling, epigenesis, embryonic development, and the evolution of language. (shrink)

The definition of biological individuality is one of the most discussed topics in philosophy of biology, but current debate has focused almost exclusively on evolution-based accounts. Moreover, several participants in this debate consider the notions of a biological individual and an organism as equivalent. In this paper, I show that the debates would be considerably enriched and clarified if philosophers took into account two elements. First, physiological fields are crucial for the understanding of biological individuality. Second, the (...) category of biological individuals should be divided into two subcategories: physiological individuals and evolutionary individuals, which suggests that the notions of organism and biological individual should not be used interchangeably. I suggest that the combination of an evolutionary and a physiological perspective will enable biologists and philosophers to supply an account of biological individuality that will be both more comprehensive and more in accordance with scientific practices. (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 paper examines the efforts in evolution research to understand form’s structure that developed in Italy during the first half of the twentieth century. In particular, it analyzes how the organic approach in biology and the study of organic form merged in the morphological research agendas of Giuseppe Colosi and Giuseppe Levi. These biologists sought to understand form’s inner composition and structure. First, I will briefly outline the morphological practices and frameworks used to study form changes and structures in the (...) early twentieth century. Second, I will discuss what the Italian biologist Antonio Pensa called the morphological problem. Third, I will examine Colosi’s response to the morphological problem. Fourth, I will analyze Levi’s morphological research program. As a result, this paper paves the way for a more nuanced and varied picture of the so-called “organicism movement” in the first half of the twentieth century by calling attention to morphology as practiced in Italian-speaking biology. In fact, alongside dialectical materialism and holistic biology, two of the main strands within organicism, the architectural approach to evolution as practiced in Italy and elsewhere had a profound impact on twentieth- and twenty-first-century organicism specifically and on evolutionary biology generally. (shrink)

Open peer commentary on the article “Circularity and the Micro-Macro-Difference” by Manfred Füllsack. Upshot: The target article defends the fundamental role of circularity for systems sciences and the necessity to develop a conceptual and methodological approach to it. The concept of circularity, however, is multifarious, and two of the main challenges in this respect are to provide distinctions between different forms of circularities and explore in detail the roles they play in organizations. This commentary provides some suggestions in this direction (...) with the aim to supplement the perspective presented in the target article with some insights from theoretical biology. (shrink)

The brain has been described as the organ of thought. In the 18th century, Pierre Cabanis notoriously claimed that “The brain secretes thought as the liver secretes bile.” For some reason, the 19th century materialist Karl Vogt believed the point needed to be made even more emphatically so he declared: “The brain secretes thought as the stomach secretes gastric juice, the liver bile, and the kidneys urine.” Countless neuroscientists make claims like the mind is the brain, or the mind is (...) the functioning brain, or the mind arises from the functioning brain. Fairly typical is a quote like the following: “Even though it is common knowledge, it never ceases to amaze me that all the richness of our mental life – all our feelings, our emotions, our thoughts, our ambitions, our love lives, our religious sentiments and even what each of us regards as his or her own intimate private self – is simply the activities of these little specks of jelly in our heads, in our brains.There is nothing else.” (Ramachandram - A Brief Tour of Human Consciousness.. (shrink)

Community databases have become crucial to the collection, ordering and retrieval of data gathered on model organisms, as well as to the ways in which these data are interpreted and used across a range of research contexts. This paper analyses the impact of community databases on research practices in model organism biology by focusing on the history and current use of four community databases: FlyBase, Mouse Genome Informatics, WormBase and The Arabidopsis Information Resource. We discuss the standards used by (...) the curators of these databases for what counts as reliable evidence, acceptable terminology, appropriate experimental set-ups and adequate materials (e.g., specimens). On the one hand, these choices are informed by the collaborative research ethos characterising most model organism communities. On the other hand, the deployment of these standards in databases reinforces this ethos and gives it concrete and precise instantiations by shaping the skills, practices, values and background knowledge required of the database users. We conclude that the increasing reliance on community databases as vehicles to circulate data is having a major impact on how researchers conduct and communicate their research, which affects how they understand the biology of model organisms and its relation to the biology of other species. (shrink)

This authored monograph introduces a genuinely theoretical approach to biology. Starting point is the investigation of empirical biological scaling including their variability, which is found in the literature, e.g. allometric relationships, fractals, etc. The book then analyzes two different aspects of biological time: first, a supplementary temporal dimension to accommodate proper biological rhythms; secondly, the concepts of protension and retention as a means of local organization of time in living organisms. Moreover, the book investigates the role (...) of symmetry in biology, in view of its ubiquitous importance in physics. In relation with the notion of extended critical transitions, the book proposes that organisms and their evolution can be characterized by continued symmetry changes, which accounts for the irreducibility of their historicity and variability. The authors also introduce the concept of anti-entropy as a measure for the potential of variability, being equally understood as alterations in symmetry. By this, the book provides a mathematical account of Gould's analysis of phenotypic complexity with respect to biological evolution. The target audience primarily comprises researchers interested in new theoretical approaches to biology, from physical, biological or philosophical backgrounds, but the book may also be beneficial for graduate students who want to enter this field. (shrink)

As the world’s population grows and urbanization continues, the global waste crisis is becoming more severe, especially in developing countries. Without proper waste management, they may encounter various environmental and health risks. Biological technologies are regarded as promising waste management and recycling approaches in developing countries due to their cost-effectiveness and capability to handle diverse waste categories. One prominent technology in this aspect is the vermicomposting of organic waste utilizing the black soldier fly larvae. Nevertheless, significant financial resources are (...) still necessary to advance and expand biological waste treatment, which requires the participation of businesses. By examining waste management companies listed on the Vietnamese stock market, we highlight two challenges that hinder the adoption and scaling of the waste treatment system using black soldier flies and potentially other biological technologies in Vietnam. Specifically, the business regards the environmental services they offer primarily as a means to generate profit rather than as a genuine commitment to environmental preservation, and the values of companies operating in the environmental sector, particularly in waste management, have been significantly undervalued by the Vietnamese investing public. Therefore, we advocate for societal shifts toward the eco-surplus culture and apply the semiconducting principle of monetary and environmental values exchange to address the problem. (shrink)

This paper emphasizes the crucial role of variation, at several different levels, for a detailed historical understanding of the development of the biomedical sciences. Going beyond valuable recent studies that focus on model organisms, experimental systems and instruments, we argue that all of these categories can be accommodated within our approach, which pays special attention to organismal and cultural variation. Our empirical examples are drawn in particular from recent historical studies of nineteenth- and early twentieth-century genetics and physiology. Based (...) on the quasi-paradoxical conclusion that biological and cultural variation both constrains and enables innovation in the biomedical sciences, we argue that more attention should be paid to variation as an analytical category in the historiography of the life sciences. (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 ArgumentThe claim that Jan Swammerdam's empirical research did not support his theory of biological preformation is shown to rest on a notion of evidence narrower than that used by many seventeenth-century natural philosophers. The principles of evidence behind the use of mechanical models are developed. It is then shown that the Cartesian theory of biological reproduction and embryology failed to gain acceptance because it did not meet the evidential requirements of these principles. The problems in this and (...) other mechanistic theories prior to Swammerdam are found to arise from certain difficulties and tensions in the mechanical conception of nature, which Swammerdam's theory is able to resolve. The relation between Swammerdam's empirical research and his theory is examined and shown to satisfy the required notion of evidence.Leibniz' puzzling appeals to Swammerdam's research in support of his metaphysical doctrine of the spontaneous development of individual substances are then examined and shown to fall within the parameters of the notion of evidence. (shrink)

The aim of this paper is to make a comparison and build up a dialogue between two different philosophical approaches to values in evolutionary biology. First, I present the approach proposed by Alexander Rosenberg and Daniel McShea in their contribution to the contemporary debate on organic progress. i.e. the idea that there has been some kind of improvement concerning organisms over the history of life. Discussing organic progress raises the question of what “better” exactly means. This requires an explicit (...) clarification on what legitimately means to speak about “good” in evolutionary biology, thus to speak about values. Second, I move on to present an approach to values that has been proposed by Georges Canguilhem in the context of a different philosophical tradition. Canguilhem’s original theses are conceived in a Darwinian framework and clearly relate to the question of values in evolutionary biology. I shall then propose a comparison between these two heterogeneous perspectives on values by critically evaluating their common points and main differences. I will argue that both perspectives agree that the question of values in evolutionary biology takes on its full meaning with respect to the relationship between the organism and the environment. However, the framework for conceptualizing values in evolutionary biology provided by Rosenberg and McShea neglects a significant point highlighted by Canguilhem, i.e. the active role that the organism can play in evaluating the environment. In line with recent developments of biology, this point can be easily integrated into Rosenberg and McShea’s framework. Finally, I will point out some main differences between the two perspectives relative to the specificity of Canguilhem’s biological philosophy. (shrink)

At the beginning of this special issue of Acta Biotheoretica carrying the above title, we present a brief overview on currently important topics that have been brought up during the last “European Conference on Mathematical and Theoretical Biology” in Edinburgh. After emphasizing the need for a “synthetic biology” also from the side of theory, model building and analysis, we survey most plenary talks of this Conference and a selected series of eigth review articles, which are mainly related to corresponding minisymposia, (...) reflecting the current state of the art and the lively discussion within this interdisciplinary field. (shrink)

This paper emphasizes the crucial role of variation, at several different levels, for a detailed historical understanding of the development of the biomedical sciences. Going beyond valuable recent studies that focus on model organisms, experimental systems and instruments, we argue that all of these categories can be accommodated within our approach, which pays special attention to organismal and cultural variation. Our empirical examples are drawn in particular from recent historical studies of nineteenth- and early twentieth-century genetics and physiology. Based (...) on the quasi-paradoxical conclusion that biological and cultural variation both constrains and enables innovation in the biomedical sciences, we argue that more attention should be paid to variation as an analytical category in the historiography of the life sciences. (shrink)

The core thesis of the paper is that the constitution of biological science begins with a conceptual innovation with far-reaching consequences with effect up to the present: by conceiving the parts of living beings as organs (that is, as tools), Aristotle laid the foundation stone for a functional explanation of animate nature. Comparative anatomy is thus transformed from a merely descriptive to an explanatory theory. The point of the discussion is above all that a functional explanation must not be (...) confused with the sort of teleology according to which the function of an organ is understood as the cause of its existence. The first section outlines the theoretical motives that Aristotle adduces in arguing for biology (against contemporary contempt for biological research). The second step addresses the significance of the parts of animals in Aristotle's larger collection of zoological material, the Historia animalium . The third section demonstrates how in the major explanatory work De partibus animalium the term organon takes on the status of a key methodological concept. Finally, the fourth section discusses the significance of the Aristotelian determination of the organic with respect to current discourses in natural science. (shrink)

Are living organisms--as Descartes argued--just machines? Or is the nature of life such that it can never be fully explained by mechanistic models? In this thought-provoking and controversial book, eminent geophysicist Walter M. Elsasser argues that the behavior of living organisms cannot be reduced to physico-chemical causality. Suggesting that molecular biology today is at the same point as Newtonian physics on the eve of the quantum revolution, Elsasser lays the foundation for a theoretical biology that points the way (...) toward a natural philosophy of organic life. Explicitly repudiating "vitalism" (the notion that the laws of nature need to be modified when applied to living organisms), Elsasser argues instead that the structural complexity of even a single living cell is "transcomputational"--that is, beyond the power of any imaginable system to compute. Beginning from this insight, Elsasser leads the reader through a step-by-step process that ultimately arrives at the conclusion that living and non-living matter are separated by "a no-man's land of irrationality." Trained in Germany as a physicist, Elsasser first pondered the implications of quantum mechanics for biology as early as 1951. The more closely he studied the inherent complexity of life, the more skeptical he became of the reductionist view of organisms as tiny machines. "An organism," he concluded, "is a source of causal chains which cannot be traced beyond a terminal point because they are lost in the unfathomable complexity of the organism." Like the physicist who works within the bounds of an unfathomable universe, Elsasser argues, the biologist must seek answers within a system that is no less unfathomable. (shrink)

This essay examines how biocentric positions assess the aims and planned products of synthetic biology. In this emerging field, scientists and engineers aim at designing and producing new life forms by various procedures. In this paper I explore whether, for biocentrists, 1) synthetic organisms have moral standing and, 2) the process of synthesising living organisms has moral implications. Because naturalness plays a role in some biocentric theories, synthetic biology — at first sight — seems to challenge the idea (...) that all living organisms have moral standing. However, according to the interpretations that I offer, the biocentric positions discussed here would also assign moral standing to synthetic organisms. That living organisms have moral standing does not necessarily imply that it is morally problematic to synthesise them. However, different lines of biocentric argumentation suggest that in designing and synthesising living organisms, the moral standing of the product needs to be taken into account. This means among other things, that according to biocentrists, such procedures may lead to special responsibilities or require certain attitudes from scientists towards their products. (shrink)

The convergence of developmental biology — embryology — and molecular biology was one of the major scientific events of the last decades of the twentieth century. The transformation of developmental biology by the concepts and methods of molecular biology has already been described. Less has been told on the reciprocal transformation of molecular biology on contact with higher organisms. The transformation of molecular biology occurred at the end of a deep crisis which affected this discipline in the sixties and (...) seventies and which led to a cruel criticism of the preexisting models of gene regulation. Numerous new, sometimes heterodox, models were proposed to describe the level at which gene regulation took place and its underlying mechanisms. The crisis resolved itself at the beginning of the eighties with the rapid accumulation of results from genetic engineering techniques and, above all, a displacement of the descriptive level from the molecule to the cell. This displacement gave molecular biologists the 'explanandum' which had been cruelly lacking during their initial study of higher organisms. The new molecular cell biology is an interfield explanation of living phenomena, relating a description and an interpretation localized at different levels of organization. (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)

It would be redundant to repeat the general thesis and specific claims advanced in the introduction. Yet in concluding I should like to draw attention to several broader themes that run through the article. One is that understanding Aristotle's biology demands attention to his psychology and metaphysics as well as to what some readers may regard as his strictly biological writings.Another is that Aristotle's views on homonymy and potentiality.

Providing a new conceptual scaffold for further research in biology and cognition, this book introduces the new field of cognitive biology, a systems biology approach showing that further progress in this field will depend on a deep recognition of developmental processes, as well as on the consideration of the developed organism as an agent able to modify and control its surrounding environment. The role of cognition, the means through which the organism is able to cope with its environment, cannot be (...) underestimated. In particular, it is shown that this activity is grounded on a theory of information based on Bayesian probabilities. The organism is considered as a cybernetic system able to integrate a processor as a source of variety (the genetic system), a regulator of its own homeostasis (the metabolic system), and a selecting system separating the self from the non-self (the membrane in unicellular organisms). Any organism is a complex system that can survive only if it is able to maintain its internal order against the spontaneous tendency towards disruption. Therefore, it is forced to monitor and control its environment and so to establish feedback circuits resulting in co-adaptation. Cognitive and biological processes are shown to be inseparable. (shrink)

Even the simplest known living organisms are complex chemical processing systems. But how sophisticated is the behaviour that arises from this? We present a framework in which even bacteria can be identified as capable of representing information in arbitrary signal molecules, to facilitate altering their behaviour to optimise their food supplies, for example. Known asion/Representation theory, this framework makes precise the relationship between physical systems and abstract concepts. Originally developed to answer the question of when a physical system is (...) computing, AR theory naturally extends to the realm of biological systems to bring clarity to questions of computation at the cellular level. (shrink)

The taxa that appear in biological classifications are commonly seen as representing information about the traits of their member organisms. This paper examines in what way taxa feature in the storage and retrieval of such information. I will argue that taxa do not actually store much information about the traits of their member organisms. Rather, I want to suggest, taxa should be understood as functioning to localize organisms in the genealogical network of life on Earth. Taxa (...) store information about where organisms are localized in the network, which is important background information when it comes to establishing knowledge about organismal traits, but it is not itself information about these traits. The view of species and higher taxa that is proposed here follows from examining three problems that occur in contemporary biological systematics and are discussed here: the problem of generalization over taxa, the problem of phylogenetic inference, and the problematic nature of the Tree of Life. (shrink)

The taxa that appear in biological classifications are commonly seen as representing information about the traits of their member organisms. This paper examines in what way taxa feature in the storage and retrieval of such information. I will argue that taxa do not actually store much information about the traits of their member organisms. Rather, I want to suggest, taxa should be understood as functioning to localize organisms in the genealogical network of life on Earth. Taxa (...) store information about where organisms are localized in the network, which is important background information when it comes to establishing knowledge about organismal traits, but it is not itself information about these traits. The view of species and higher taxa that is proposed here follows from examining three problems that occur in contemporary biological systematics and are discussed here: the problem of generalization over taxa, the problem of phylogenetic inference, and the problematic nature of the Tree of Life. (shrink)

Synthetic organisms are at the same time organisms and artifacts. In this paper we aim to determine whether such entities have a good of their own, and so are candidates for being directly morally considerable. We argue that the good of non-sentient organisms is grounded in an etiological account of teleology, on which non-sentient organisms can come to be teleologically organized on the basis of their natural selection etiology. After defending this account of teleology, we argue (...) that there are no grounds for excluding synthetic organisms from having a good also grounded in their teleological organization. However, this comes at a cost; traditional artifacts will also be seen as having a good of their own. We defend this as the best solution to the puzzle about what to say about the good of synthetic organisms. (shrink)

The genetic code appeared on Earth at the origin of life, and the codes of culture arrived almost four billion years later. For a long time it has been assumed that these are the only codes that exist in Nature, and if that were true we would have to conclude that codes are extraordinary exceptions that appeared only at the beginning and at the end of the history of life. In reality, various other organic codes have been discovered in the (...) past few decades and it is likely that more will come to light in the future. The existence of many organic codes in Nature is therefore an experimental fact, but also more than that. It is one of those facts that have extraordinary implications. In this book it is shown that the genetic code was a precondition for the origin of the first cells, the signal transduction codes divided the first cells into three primary kingdoms (Archaea, Bacteria and Eukarya), the splicing codes were instrumental to the origin of the eukaryotic nucleus, the histone code provided a new regulation system in eukaryotic genomes, and the cytoskeleton codes allowed the Eukarya to perform internal movements, including those of mitosis and meiosis. It is shown, furthermore, that organic codes had a key role in multicellular life, in particular in the origin of animals, the origin of mind and the origin of language. The great events of macroevolution, in other words, were associated with the appearance of new organic codes, and we can easily understand why. The reason is that a new code brings into existence something that has never existed before because it creates arbitrary associations, relationships that are not determined by physical necessity. Another outstanding implication is the fact that codes involve meaning and we need therefore to introduce in biology, with the standard methods of science, not only the concept of biological information but also that of biological meaning. The research on biological codes, in conclusion, is bringing to light new mechanisms in evolution and new fundamental concepts in science. This research is the field of Code Biology, the study of all codes of life, from the genetic code to the codes of culture, from the origin of life to the origin of man. (shrink)

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

It is worthwhile comparing Hylomorphic and Animalistic accounts of personal identity since they both identify the human animal and the human person.The topics of comparison will be three: The first is accounting for our intuitions in cerebrum transplant and irreversible coma cases. Hylomorphism, unlike animalism, appears to capture “commonsense” beliefs here, preserves the maxim that identity matters, and does not run afoul of the Only x and y rule. The next topic of comparison reveals how the rival explanations of transplants (...) and comas are both at odds with some compelling biological assumptions. The third issue deals with our practical concerns, most notably, the possibility of an afterlife. It turns out that the hylomorphic treatment of Purgatory raises the spectra of the “too many thinkers” problem and some considerable unfairness. Contrary to expectations, an animalist insistence on uninterrupted bodily continuity between this life and the next does not involve deceptive body snatching. (shrink)

According to new mechanists, mechanisms explain how specific biological phenomena are produced. New mechanists have had little to say about how mechanisms relate to the organism in which they reside. A key feature of organisms, emphasized by the autonomy tradition, is that organisms maintain themselves. To do this, they rely on mechanisms. But mechanisms must be controlled so that they produce the phenomena for which they are responsible when and in the manner needed by the organism. To (...) account for how they are controlled, we characterize mechanisms as sets of constraints on the flow of free energy. Some constraints are flexible and can be acted on by other mechanisms, control mechanisms, that utilize information procured from the organism and its environment to alter the flexible constraints in other mechanisms so that they produce phenomena appropriate to the circumstances. We further show that control mechanisms in living organisms are organized heterarchically—control is carried out primarily by local controllers that integrate information they acquire as well as that which they procure from other control mechanisms. The result is not a hierarchy of control but an integrated network of control mechanisms that has been crafted over the course of evolution. (shrink)

Thomas Kuhn described the progress of science as comprising occasional paradigm shifts separated by interludes of ‘normal science’. The paradigm that has held sway since the inception of molecular biology is that genes (mainly) encode proteins. In parallel, theoreticians posited that mutation is random, inferred that most of the genome in complex organisms is non‐functional, and asserted that somatic information is not communicated to the germline. However, many anomalies appeared, particularly in plants and animals: the strange genetic phenomena of (...) paramutation and transvection; introns; repetitive sequences; a complex epigenome; lack of scaling of (protein‐coding) genes and increase in ‘noncoding’ sequences with developmental complexity; genetic loci termed ‘enhancers’ that control spatiotemporal gene expression patterns during development; and a plethora of ‘intergenic’, overlapping, antisense and intronic transcripts. These observations suggest that the original conception of genetic information was deficient and that most genes in complex organisms specify regulatory RNAs, some of which convey intergenerational information. Also see the video abstract here: https://youtu.be/qxeGwahBANw. (shrink)

This paper uses the framework of Formal Darwinism (FD) to evaluate organism-centric critiques of the Modern Synthesis (MS). The first section argues that the FD project reconciles two kinds of selective explanations in biology. Thus it is not correct to say that the MS neglects organisms—instead, it explains organisms’ design, as argued in the second section. In the third section I employ a concept of the organism derived from Kant that has two aspects: the parts presupposing the whole, (...) and the productivity of the parts in relation to the whole. The first aspect corresponds to the “design” that FD explains, whereas the second aspect is something about which the MS is largely silent. (shrink)

Modern biology gives many casuistic descriptions of mutual informational interconnections between organisms. Semiotic and hermeneutic processes in biosphere require a set of “sentient” community of players who optimize their living strategies to be able to stay in game. Perceptible surfaces of the animals, semantic organs, represent a special communicative interface that serves as an organ of self-representation of organic inwardness. This means that theinnermost dimensions and potentialities of an organism may enter the senses of other living being when effectively (...) expressed on the outermost surfaces of theformer and meaningfully interpreted by the later. Moreover, semantic organs do not exist as objectively describable entities. They are always born via interpretative act and their actual form depends on both the potentialities of body plan of a bearer and the species-specific interpretation of a receiver. As such the semantic organs represent an important part of biological reality and thus deserve to be contextualized within existing comparative vocabulary. Here we argue that the study of the organic self-representation has a key importance for deeper insight into the evolution of communicative coupling among living beings. (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)

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)