Traditionally, it has been supposed that the central object of Biology are ‘organisms’. The expression “organism” is relatively recent in the use that it has nowadays –it was introduced by the authors of the German Idealism– but corresponds to a very traditional notion. An ‘organism’ is a substance composed by a plurality of materials organized by the same substance that acts upon itself to persist in time, in order to a finality that is the organism itself. To make intelligible (...) an organism seems indispensable its order to an end. This teleological perspective, nevertheless, is unacceptable for the reductivist perspective of Biology, prevalent since the triumph of what has been called the “Modern Synthesis” the first half of last century. It has been proposed, for that reason, to substitute the traditional idea of ‘organism’ by that of ‘Darwinian individual’ (cf. Godfrey-Smith, 2009), that could offer a more adequate perspective of the object of Biology. The object of this science could not be organisms, but individuals that can enter the Darwinian evolutionary drift. In this work it is explained why a hiatus persists between organisms teleologically oriented and a Darwinian individual. The Darwinian perspective leaves aside the central character of the object of Biology: life. (shrink)

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)

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)

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)

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)

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)

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)

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)

Model organisms are at the centre of progress in biology but attributing them an excessive representational power and concentrating on a limited group of them, although efficient for research, can have negative consequences, mainly of epistemic nature. Here, I argue that model organisms are exploratory models with a perspectival modelling function, and that a deflated representational power is needed for their proper use. In support of this argument, I will analyse developmental biology as a case study. Firstly, I (...) show that model organisms in developmental biology are not selected because of their representational capabilities, but mainly based on practical criteria. Secondly, I defend that the epistemic organization of developmental biology around questions fosters exploration and perspectival modelling and I propose that developmental biology is a ‘model organism situated knowledge’. Lastly, I use the study of the mechanisms of cell fate acquisition during early embryonic development in _C. elegans_ and mice as a case study to illustrate how a plurality of model organisms allows exploration and perspectival modelling. The use of model organisms for exploration and perspectival modelling, with a limited representational power, should allow more adequate inferences about human embryonic development and encourage the introduction of more model organisms for a comprehensive navigation of the space of possibilities. (shrink)

Synthetic biology makes use of genetic and other materials derived from modern biological life forms to design and construct novel synthetic organisms. Artificial organisms are not constructed from parts of existing biological organisms, but from non-biological materials. Artificial and synthetic organisms are artefactual organisms. Here we are concerned with the non-instrumental value of such organisms. More specifically, we are concerned with the extent to which artefactual organisms have natural value, inherent (...) worth and intrinsic value. Our conclusions are largely supportive of the value of artefactual organisms. However, they do not constitute a comprehensive ethical evaluation of them. (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)

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)

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)

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)

Systems Biology and the Modern Synthesis are recent versions of two classical biological paradigms that are known as structuralism and functionalism, or internalism and externalism. According to functionalism (or externalism), living matter is a fundamentally passive entity that owes its organization to external forces (functions that shape organs) or to an external organizing agent (natural selection). Structuralism (or internalism), is the view that living matter is an intrinsically active entity that is capable of organizing itself from within, with purely (...) internal processes that are based on mathematical principles and physical laws. At the molecular level, the basic mechanism of the Modern Synthesis is molecular copying, the process that leads in the short run to heredity and in the long run to natural selection. The basic mechanism of Systems Biology, instead, is self-assembly, the process by which many supramolecular structures are formed by the spontaneous aggregation of their components. In addition to molecular copying and self-assembly, however, molecular biology has uncovered also a third great mechanism at the heart of life. The existence of the genetic code and of many other organic codes in Nature tells us that molecular coding is a biological reality and we need therefore a framework that accounts for it. This framework is Code biology, the study of the codes of life, a new field of research that brings to light an entirely new dimension of the living world and gives us a completely new understanding of the origin and the evolution 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)

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)

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)

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)

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 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.

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)

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 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)

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)

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)

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)

Many biologists still believe in a sort of post-Cartesian foundation of reality wherein objects are independent of subjects which cognize them. Recent research in behaviour, cognition, and psychology, however, provides plenty of evidence to the effect that the perception of an object differs depending on the kind of animal observer, and also its personality, hormonal, and sensorial set-up etc. In the following, I argue that exposed surfaces of organisms interact with other organisms’ perception to form semiautonomous relational entities (...) called semantic organs, which participate in biological reality as discrete heritable evolutionary units. The inner dimensions and potentialities of an organism can enter the senses of another living being when effectively expressed on the outer surfaces of the former and meaningfully perceived by the latter. Semantic organs have three basic sources of variability: intrinsic, i.e., genetic, epigenetic, and developmental processes; extrinsic, meaning the biotic and abiotic environmental conditions which affect the developmental generators of intrinsic variability; and perceptual, stemming from differences in the subject-specific interpretation of a SO’s structural basis. Extrinsic and intrinsic sources of variability are, however, just precursors to semantic organs. SOs are relational entities which always come into existence through an act of perception and their actual form depends both on the physical potentialities of the bearer and the species- or group-specific interpretation of the receiver. (shrink)

Biology on this planet represents an astonishing experiment in carbon‐based chemistry which, over billions of years, has generated billions of species adapted to countless major and minor fluctuations in ecological circumstances. In one sense there is no way to generalize about biology. While biological activities can all be ultimately explained by physical laws (like everything else in the universe), it is the emergent intensely particular properties of organisms that most interest us. This essay represents an attempt to describe (...) some of the more prominent patterns that emerge from the sea of biological particularities, patterns that present many opportunities for religous reflection. (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)

Complex organisms thwart the simple rectilinear causality paradigm of “necessary and sufficient,” with its experimental strategy of “knock down and overexpress.” This Essay organizes the eccentricities of biology into four categories that call for new mathematical approaches; recaps for the biologist the philosopher's recent refinements to the causation concept and the mathematician's computational tools that handle some but not all of the biological eccentricities; and describes overlooked insights that make causal properties of physical hierarchies such as emergence and (...) downward causation straightforward. Reviewing and extrapolating from similar situations in physics, it is suggested that new mathematical tools for causation analysis incorporating feedback, signal cancellation, nonlinear dependencies, physical hierarchies, and fixed constraints rather than instigative changes will reveal unconventional biological behaviors. These include “eigenisms,” organisms that are limited to quantized states; trajectories that steer a system such as an evolving species toward optimal states; and medical control via distributed “sheets” rather than single control points. (shrink)

Synthetic biology aims at making life easier to an engineer by applying biotechnology engineering principles such as standardization and modularity. I argue that living organisms are inherently non-machine, non-standardized entities and that the current state-of-the-art in SynBio combines pre- and post-standardization efforts, in a scenario without evidence that full standardization in biology is even possible. I finally propose a new view on SynBio based on purpose rather than on technicalities.

The evolution of economic altruism is one of the most vigorous areas of study at the intersection of biology, economics, and philosophy. The basic problem is easily understood. Biological organisms, be they people or paramecia, have ample opportunity to confer benefits on others at relatively low cost to themselves. If conferring such benefits becomes common, the overall productivity of the population in which it occurs is increased. Presumably, there is no advantage to refusing such benefits, but it is (...) also the case that there is considerable advantage to pursuing a strategy according to which such benefits are accepted, but not conferred. In populations where individuals interact at random with others and when individuals play pure strategies (i.e., they always confer or do not confer benefits), the inevitable outcome is that altruistic behavior is driven to extinction. (Axelrod 1984) Nonetheless, there is ample evidence that self-sacrificing behavior is common in nature. (Sober and Wilson 1998) Consequently, individuals must not be interacting at random. The pressing question is then: what patterns of non-random interaction are responsible for the prevalence of altruistic behavior, and more theoretically, what sorts of plausible mechanisms exist that could generate the right kind of non- 1 The research reported here was supported by Canada ????? grant # ????? and the Centre for Applied Ethics at the University of British Columbia. (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)

Over his philosophical career, David Wiggins has produced a body of work that, though varied and wide-ranging, stands as a coherent and carefully integrated whole. In this book Ferner examines Wiggins’ conceptualist-realism, his sortal theory ‘D’ and his human being theory in order to assess how far these elements of his systematic metaphysics connect. In addition to rectifying misinterpretations and analysing the relations between Wiggins’ works, Ferner reveals the importance of the philosophy of biology to Wiggins’ approach. This book elucidates (...) the biological anti-reductionism present in Wiggins’ work and highlights how this stance stands as a productive alternative to emergentism. With an analysis of Wiggins’ construal of substances, specifically organisms, the book goes on to discuss how Wiggins brings together the concept of a person with the concept of a natural substance, or human being. An extensive introduction to the work of David Wiggins, as well as a contribution to the dialogue between personal identity theorists and philosophers of biology, this book will appeal to students and scholars working in the areas of philosophy, biology and the history of Anglophone metaphysics. (shrink)

Predictions about the health risks of low level radiation combine two sorts of measures. One estimates the amount and kinds of radiation released into the environment, and the other estimates the adverse health effects. A new field called health physics integrates and applies nuclear physics to cytology to supply both these estimates. It does so by first determining the kinds of effects different types of radiation produce in biological organisms, and second, by monitoring the extent of these effects (...) produced by given levels of exposure. This essay examines the interplay between evidential constraints and external, contextual interests and values in studying the biological hazards of radiation. By analyzing the debate over linear vs. quadratic dose response models, the essay focuses on problems of developing quantitative, rather than qualitative, estimates of the risks of increased cancer incidence in an exposed population. (shrink)

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)

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

This book provides a detailed analysis of Aristotle's Parts of Animals. It takes its bearings from the detailed natural history observations that inform, and in many ways penetrate, the philosophical argument. This analysis raises the question of how easy it is to clearly disentangle what some might describe as the "merely" biological from the philosophical. This book explores the notion and consequences of describing the activity in which Aristotle is engaged as philosophical biology. Do readers of Aristotle have in (...) mind organisms like sea squirts (ascidians) or sea cucumbers (holuthurians) when trying to understand Aristotle's argument regarding plant-like animals? Do we need the phenomena in front of us to understand the terms of the philosophical argument in a richer way? The discussion of plant-like animals is important to Aristotle because of the apparent continuum between plant and animal life. Where does Aristotle draw the line? Plant-like animals bring this question into focus and demonstrate the indeterminacy of any potential solution to the division. This analysis of the Parts of Animals shows that the study of the nature of the organic world was Aristotle's way into such ontological problems as the relationship between matter and form, the interplay between form and function, and the heterogeneity of the many different kinds of being. (shrink)