“Impermanent Biological Phenomena” July 2021, Buddhism and Culture (a Korean-language Buddhist magazine sponsored by the Foundation for the Promotion of Korean Buddhism), Korea.

This third paper locates the synthetic neurorobotics research reviewed in the second paper in terms of themes introduced in the first paper. It begins with biological non-reductionism as understood by Searle. It emphasizes the role of synthetic neurorobotics studies in accessing the dynamic structure essential to consciousness with a focus on system criticality and self, develops a distinction between simulated and formal consciousness based on this emphasis, reviews Tani and colleagues' work in light of this distinction, and ends by (...) forecasting the increasing importance of synthetic neurorobotics studies for cognitive science and philosophy of mind going forward, finally in regards to most- and myth-consciousness. (shrink)

Direct neurological and especially imaging-driven investigations into the structures essential to naturally occurring cognitive systems in their development and operation have motivated broadening interest in the potential for artificial consciousness modeled on these systems. This first paper in a series of three begins with a brief review of Boltuc’s (2009) “brain-based” thesis on the prospect of artificial consciousness, focusing on his formulation of h-consciousness. We then explore some of the implications of brain research on the structure of consciousness, finding limitations (...) in biological approaches to the study of consciousness. Looking past these limitations, we introduce research in artificial consciousness designed to test for the emergence of consciousness, a phenomenon beyond the purview of the study of existing biological systems. (shrink)

1900 was a remarkable year for science. Several ground-breaking events took place, in physics, biology and psychology. Planck introduced the quantum concept, the work of Mendel was rediscovered, and Sigmund Freud published The Interpretation of Dreams . These events heralded the emergence of completely new areas of inquiry, all of which greatly affected the intellectual landscape of the 20 th century, namely quantum physics, genetics and psychoanalysis. What do these developments have in common? Can we discern a family likeness, a (...) basic affinity between them, so that we can use the one to deepen our understanding of the other? One common denominator is that they open up realms of inquiry that are significantly different from the world of everyday experience, namely the realm of elementary particles, of genes and genomes, and of the unconscious. But to what extent can we meaningfully argue, for instance, that the genome is the biological unconscious, and the unconscious the psychic genome? To address these questions, I will build on the work of two key intellectual figures who have explored the affinities of these developments in depth, namely Erwin Schrödinger (a quantum physicist and avid reader of Schopenhauer who initiated molecular biology) and Jacques Lacan (who reframed the specificity of psychoanalysis with the help of 20 th century science: the era of structural linguistics, but also of quantum physics, molecular biology, bioinformatics and DNA). (shrink)

An influential position in the philosophy of biology claims that there are no biological laws, since any apparently biological generalization is either too accidental, fact-like or contingent to be named a law, or is simply reducible to physical laws that regulate electrical and chemical interactions taking place between merely physical systems. In the following I will stress a neglected aspect of the debate that emerges directly from the growing importance of mathematical models of biological phenomena. My main (...) aim is to defend, as well as reinforce, the view that there are indeed laws also in biology, and that their difference in stability, contingency or resilience with respect to physical laws is one of degrees, and not of kind . (shrink)

This selective review explores biologically inspired learning as a model for intelligent robot control and sensing technology on the basis of specific examples. Hebbian synaptic learning is discussed as a functionally relevant model for machine learning and intelligence, as explained on the basis of examples from the highly plastic biological neural networks of invertebrates and vertebrates. Its potential for adaptive learning and control without supervision, the generation of functional complexity, and control architectures based on self-organization is brought forward. Learning (...) without prior knowledge based on excitatory and inhibitory neural mechanisms accounts for the process through which survival-relevant or task-relevant representations are either reinforced or suppressed. The basic mechanisms of unsupervised biological learning drive synaptic plasticity and adaptation for behavioral success in living brains with different levels of complexity. The insights collected here point toward the Hebbian model as a choice solution for “intelligent” robotics and sensor systems. Keywords: Hebbian learning; synaptic plasticity; neural networks; self-organization; brain; reinforcement; sensory processing; robot control . (shrink)

Several authors have used the notion of causal specificity in order to defend non-parity about genetic causes (Waters 2007, Woodward 2010, Weber 2017, forthcoming). Non-parity in this context is the idea that DNA and some other biomolecules that are often described as information-bearers by biologists play a unique role in life processes, an idea that has been challenged by Developmental Systems Theory (e.g., Oyama 2000). Indeed, it has proven to be quite difficult to state clearly what the alleged special role (...) of genetic causes consists in. In this paper, I show that the set of biomolecules that are normally considered to be information-bearers (DNA, mRNA) can be shown to be the most specific causes of protein primary structure, provided that causal specificity is measured over a relevant space of biological possibilities, disregarding physical as well as logically possible states of the causal variables. (shrink)

Biological atomism postulates that all life is composed of elementary and indivisible vital units. The activity of a living organism is thus conceived as the result of the activities and interactions of its elementary constituents, each of which individually already exhibits all the attributes proper to life. This paper surveys some of the key episodes in the history of biological atomism, and situates cell theory within this tradition. The atomistic foundations of cell theory are subsequently dissected and discussed, (...) together with the theory’s conceptual development and eventual consolidation. This paper then examines the major criticisms that have been waged against cell theory, and argues that these too can be interpreted through the prism of biological atomism as attempts to relocate the true biological atom away from the cell to a level of organization above or below it. Overall, biological atomism provides a useful perspective through which to examine the history and philosophy of cell theory, and it also opens up a new way of thinking about the epistemic decomposition of living organisms that significantly departs from the physicochemical reductionism of mechanistic biology. (shrink)

Since Boorse [Philos Sci 44(4):542–573, 1977] published his paper “Health as a theoretical concept” one of the most lively debates within philosophy of medicine has been on the question of whether health and disease are in some sense ‘objective’ and ‘value-free’ or ‘subjective’ and ‘value-laden’. Due to the apparent ‘failure’ of pure naturalist, constructivist, or normativist accounts, much in the recent literature has appealed to more conciliatory approaches or so-called ‘hybrid accounts’ of health and disease. A recent paper by Matthewson (...) and Griffiths [J Med Philos 42(4):447–466, 2017], however, may bear the seeds for the revival of purely naturalist approach to health and disease. In this paper, I defend their idea of Biological Normativity against recent criticism by Schwartz [J Med Philos Forum Bioethics Philos Med 42(4):485–502, 2017] and hope to help it flower into a revival of naturalist approaches in the philosophy of medicine. (shrink)

Although contemporary metaphysics has recently undergone a neo-Aristotelian revival wherein dispositions, or capacities are now commonplace in empirically grounded ontologies, being routinely utilised in theories of causality and modality, a central Aristotelian concept has yet to be given serious attention – the doctrine of hylomorphism. The reason for this is clear: while the Aristotelian ontological distinction between actuality and potentiality has proven to be a fruitful conceptual framework with which to model the operation of the natural world, the distinction between (...) form and matter has yet to similarly earn its keep. In this chapter, I offer a first step toward showing that the hylomorphic framework is up to that task. To do so, I return to the birthplace of that doctrine - the biological realm. Utilising recent advances in developmental biology, I argue that the hylomorphic framework is an empirically adequate and conceptually rich explanatory schema with which to model the nature of organisms. (shrink)

Synthetic biologists aim to generate biological organisms according to rational design principles. Their work may have many beneficial applications, but it also raises potentially serious ethical concerns. In this article, we consider what attention the discipline demands from bioethicists. We argue that the most important issue for ethicists to examine is the risk that knowledge from synthetic biology will be misused, for example, in biological terrorism or warfare. To adequately address this concern, bioethics will need to broaden its (...) scope, contemplating not just the means by which scientific knowledge is produced, but also what kinds of knowledge should be sought and disseminated. (shrink)

The impressive variation amongst biological individuals generates many complexities in addressing the simple-sounding question what is a biological individual? A distinction between evolutionary and physiological individuals is useful in thinking about biological individuals, as is attention to the kinds of groups, such as superorganisms and species, that have sometimes been thought of as biological individuals. More fully understanding the conceptual space that biological individuals occupy also involves considering a range of other concepts, such as life, (...) reproduction, and agency. There has been a focus in some recent discussions by both philosophers and biologists on how evolutionary individuals are created and regulated, as well as continuing work on the evolution of individuality. (shrink)

The selected effects or ‘etiological’ theory of Proper function is a naturalistic and realist account of biological teleology. It is used to analyse normativity in philosophy of language, philosophy of mind, philosophy of medicine and elsewhere. The theory has been developed with a simple and intuitive view of natural selection. Traits are selected because of their positive effects on the fitness of the organisms that have them. These ‘selected effects’ are the Proper functions of the traits. Proponents argue that (...) this analysis of biological teleology has the unique advantage that the selected effect function of a trait is also a causal explanation of the trait: the trait exists because it performs this function. We show, however, that selected effect functions as currently defined explain the existence of traits only under highly restrictive assumptions about evolutionary dynamics. In many common scenarios in which traits evolve by natural selection, selected effect functions do not explain those traits. This is because definitions of selected effect function extract from any evolutionary scenario only the information that would be explanatorily relevant in the simple evolutionary scenario implicit in those definitions. When applied to more complex scenarios selected effect functions omit the key information that is explanatorily relevant in those scenarios. The assumptions required for selected effect functions to be explanatory are particularly unlikely to hold in the domain that its proponents care most about - the evolution of representation. A more adequate selected effects theory of Proper functions may be possible, but will require much greater attention to the structure of actual evolutionary explanations. (shrink)

Absolute needs (as against instrumental needs) are independent of the ends, goals and purposes of personal agents. Against the view that the only needs are instrumental needs, David Wiggins and Garrett Thomson have defended absolute needs on the grounds that the verb ‘need’ has instrumental and absolute senses. While remaining neutral about it, this article does not adopt that approach. Instead, it suggests that there are absolute biological needs. The absolute nature of these needs is defended by appeal to: (...) their objectivity (as against mind-dependence); the universality of the phenomenon of needing across the plant and animal kingdoms; the impossibility that biological needs depend wholly upon the exercise of the abilities characteristic of personal agency; the contention that the possession of biological needs is prior to the possession of the abilities characteristic of personal agency. Finally, three philosophical usages of ‘normative’ are distinguished. On two of these, to describe a phenomenon or claim as ‘normative’ is to describe it as value-dependent. A description of a phenomenon or claim as ‘normative’ in the third sense does not entail such value-dependency, though it leaves open the possibility that value depends upon the phenomenon or upon the truth of the claim. It is argued that while survival needs (or claims about them) may well be normative in this third sense, they are normative in neither of the first two. Thus, the idea of absolute need is not inherently normative in either of the first two senses. (shrink)

García-Barranquero et al explore the desirability of human ageing. They differentiate between chronological and biological views of ageing and contend that the positive aspects of ageing are solely linked to chronological ageing. Consequently, the authors embrace the potential for technological interventions in biological ageing. Contrary to their stance, I argue that there are sometimes desirable aspects associated with biological ageing. Therefore, proposals aiming to eliminate, mitigate or diminish biological ageing are not without problems.

Is it possible to know anything about life we have not yet encountered? We know of only one example of life: our own. Given this, many scientists are inclined to doubt that any principles of Earth’s biology will generalize to other worlds in which life might exist. Let’s call this the “N = 1 problem.” By comparison, we expect the principles of geometry, mechanics, and chemistry would generalize. Interestingly, each of these has predictable consequences when applied to biology. The surface-to-volume (...) property of geometry, for example, limits the size of unassisted cells in a given medium. This effect is real, precise, universal, and predictive. Furthermore, there are basic problems all life must solve if it is to persist, such as resistance to radiation, faithful inheritance, and energy regulation. If these universal problems have a limited set of possible solutions, some common outcomes must consistently emerge. In this chapter, I discuss the N = 1 problem, its implications, and my response (Mariscal 2014). I hold that our current knowledge of biology can justify believing certain generalizations as holding for life anywhere. Life on Earth may be our only example of life, but this is only a reason to be cautious in our approach to life in the universe, not a reason to give up altogether. In my account, a candidate biological generalization is assessed by the assumptions it makes. A claim is accepted only if its justification includes principles of evolution, but no contingent facts of life on Earth. (shrink)

In this paper I first offer a systematic outline of a series of conceptual novelties in the life-sciences that have favoured, over the last three decades, the emergence of a more social view of biology. I focus in particular on three areas of investigation: (1) technical changes in evolutionary literature that have provoked a rethinking of the possibility of altruism, morality and prosocial behaviours in evolution; (2) changes in neuroscience, from an understanding of the brain as an isolated data processor (...) to the ultrasocial and multiply connected social brain of contemporary neuroscience; and (3) changes in molecular biology, from the view of the gene as an autonomous master of development to the ‘reactive genome’ of the new emerging field of molecular epigenetics. In the second section I reflect on the possible implications for the social sciences of this novel biosocial terrain and argue that the postgenomic language of extended epigenetic inheritance and blurring of the nature/nurture boundaries will be as provocative for neo-Darwinism as it is for the social sciences as we have known them. Signs of a new biosocial language are emerging in several social-science disciplines and this may represent an exciting theoretical novelty for twenty-first social theory. (shrink)

Modern life sciences research is increasingly relying on artificial intelligence (AI) approaches to model biological systems, primarily centered around the use of machine learning (ML) models. Although ML is undeniably useful for identifying patterns in large, complex data sets, its widespread application in biological sciences represents a significant deviation from traditional methods of scientific inquiry. As such, the interplay between these models and scientific understanding in biology is a topic with important implications for the future of scientific research, (...) yet it is a subject that has received little attention. Here, we draw from an epistemological toolkit to contextualize recent applications of ML in biological sciences under modern philosophical theories of understanding, identifying general principles that can guide the design and application of ML systems to model biological phenomena and advance scientific knowledge. We propose that conceptions of scientific understanding as information compression, qualitative intelligibility, and dependency relation modelling provide a useful framework for interpreting ML-mediated understanding of biological systems. Through a detailed analysis of two key application areas of ML in modern biological research – protein structure prediction and single cell RNA-sequencing – we explore how these features have thus far enabled ML systems to advance scientific understanding of their target phenomena, how they may guide the development of future ML models, and the key obstacles that remain in preventing ML from achieving its potential as a tool for biological discovery. Consideration of the epistemological features of ML applications in biology will improve the prospects of these methods to solve important problems and advance scientific understanding of living systems. (shrink)

A biologically unavoidable sequence is an infinite gender sequence which occurs in every gendered, infinite genealogical network satisfying certain tame conditions. We show that every eventually periodic sequence is biologically unavoidable (this generalizes König's Lemma), and we exhibit some biologically avoidable sequences. Finally we give an application of unavoidable sequences to cellular automata.

This chapter sets the scene for the subsequent philosophical discussions by surveying a number of biological interventions that have been used, or might in the future be used, for the purposes of crime prevention. These interventions are pharmaceutical interventions intended to suppress libido, treat substance abuse or attention deficit-hyperactivity disorder (ADHD), or modulate serotonin activity; nutritional interventions; and electrical and magnetic brain stimulation. Where applicable, we briefly comment on the historical use of these interventions, and in each case we (...) discuss the evidence that they are effective, or might become so with further refinement. The chapter concludes with a comment on some potentially significant differences between the varieties of intervention that we canvass. (shrink)

Synthetic biology is a field of research that concentrates on the design, construction, and modification of new biomolecular parts and metabolic pathways using engineering techniques and computational models. By employing knowledge of operational pathways from engineering and mathematics such as circuits, oscillators, and digital logic gates, it uses these to understand, model, rewire, and reprogram biological networks and modules. Standard biological parts with known functions are catalogued in a number of registries (e.g. Massachusetts Institute of Technology Registry of (...) Standard Biological Parts). Biological parts can then be selected from the catalogue and assembled in a variety of combinations to construct a system or pathway in a microbe. Through the innovative re-engineering of biological circuits and the optimization of certain metabolic pathways, biological modules can be designed to reprogram organisms to produce products or behaviors. Synthetic biology is what is known as a “platform technology”. That is, it generates highly transferrable theoretical models, engineering principles, and know-how that can be applied to create potential products in a wide variety of industries. Proponents suggest that applications of synthetic biology may be able to provide scientific and engineered solutions to a multitude of worldwide problems from health to energy. Synthetic biology research has already been successful in constructing microbial products which promise to offer cheaper pharmaceuticals such as the antimalarial synthetic drug artemisinin, engineered microbes capable of cleaning up oil spills, and the engineering of biosensors that can detect the presence of high concentrations of arsenic in drinking water. One of the potential benefits of synthetic biology research is in its application to biofuel production. It is this application which is the focus of this entry. The term “biofuel” has referred generally to all liquid fuels that are sourced from plant or plant byproducts and are used for energy necessary for transportation vehicles (Thompson 2012). Biofuels that are produced using synthetic biological techniques re-engineer microbes into biofuel factories are a subset of these. (shrink)

In recent years, a proliferation of books about empathy, cooperation and pro-social behaviours (Brooks, 2011a) has significantly influenced the discourse of the life-sciences and reversed consolidated views of nature as a place only for competition and aggression. In this article I describe the recent contribution of three disciplines – moral psychology (Jonathan Haidt), primatology (Frans de Waal) and the neuroscience of morality – to the present transformation of biology and evolution into direct sources of moral phenomena, a process here named (...) the ‘moralization of biology’. I conclude by addressing the ambivalent status of this constellation of authors, for whom today ‘morality comes naturally’: I explore both the attractiveness of their message, and the problematic epistemological assumptions of their research programmes in the light of new discoveries in developmental and molecular biology. (shrink)

The theory of evolution, which provides the conceptual framework for all modern research in organismal biology and informs research in molecular bi- ology, has gone through several stages of expansion and refinement. Darwin and Wallace (1858) of course proposed the original idea, centering on the twin concepts of natural selection and common descent. Shortly thereafter, Wallace and August Weismann worked toward the complete elimination of any Lamarckian vestiges from the theory, leaning in particular on Weismann’s (1893) concept of the separation (...) of soma and germ, resulting in what is some- times referred to as “neo-Darwinism”. (shrink)

Neo-Aristotelian ethical naturalism aims to place moral virtue in the natural world by showing that moral goodness is an instance of natural goodness—a kind of goodness supposedly also found in the biological realm of plants and non-human animals. One of the central issues facing neo-Aristotelian naturalists concerns their commitment to a kind of function ascription based on the concept of the flourishing of an organism that seems to have no place in modern biology. In this paper, I offer a (...) novel defense of this functional commitment by appealing to the organizational account of biological function. I argue that the flourishing-based concept of function that forms the basis of the neo-Aristotelian account of natural goodness is explanatorily indispensable to biology, and therefore essential to the understanding of living things. (shrink)

Stephen Hawking’s caution against messaging extraterrestrial intelligence is a claim of universal biology and is probably false.

In this essay, we discuss Simona Ginsburg and Eva Jablonka’s The Evolution of the Sensitive Soul from an interdisciplinary perspective. Constituting perhaps the longest treatise on the evolution of consciousness, Ginsburg and Jablonka unite their expertise in neuroscience and biology to develop a beautifully Darwinian account of the dawning of subjective experience. Though it would be impossible to cover all its content in a short book review, here we provide a critical evaluation of their two key ideas—the role of Unlimited (...) Associative Learning in the evolution of, and detection of, consciousness and a metaphysical claim about consciousness as a mode of being—in a manner that will hopefully overcome some of the initial resistance of potential readers to tackle a book of this length. (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)

We argue that genuine biological autonomy, or described at human level as free will, requires taking into account quantum vacuum processes in the context of biological teleology. One faces at least three basic problems of genuine biological autonomy: (1) if biological autonomy is not physical, where does it come from? (2) Is there a room for biological causes? And (3) how to obtain a workable model of biological teleology? It is shown here that the (...) solution of all these three problems is related to the quantum vacuum. We present a short review of how this basic aspect of the fundamentals of quantum theory, although it had not been addressed for nearly 100 years, actually it was suggested by Bohr, Heisenberg, and others. Realizing that the quantum mechanical measurement problem associated with the “collapse” of the wave function is related, in the Copenhagen Interpretation of quantum mechanics, to a process between self-consciousness and the external physical environment, we are extending the issue for an explanation of the different processes occurring between living organisms and their internal environment. Definitions of genuine biological autonomy, biological aim, and biological spontaneity are presented. We propose to improve the popular two-stage model of decisions with a biological model suitable to obtain a deeper look at the nature of the mind-body problem. In the newly emerging picture biological autonomy emerges as a new, fundamental and inevitable element of the scientific worldview. (shrink)

Waters’s (2007) actual difference making and Weber’s (2013, 2017) biological normality approaches to causal selection have received many criticisms, some of which miss their target. Disagreement about whether Waters’s and Weber’s views succeed in providing criteria that uniquely singles out the gene as explanatorily significant in biology has led philosophers to overlook a prior problem. Before one can address whether Waters’s and Weber’s views successfully account for the explanatory significance of genes, one must ask whether either view satisfactorily meets (...) the necessary conditions for causal selection in the first place. An adequate defense of causal selection must meet two desiderata. First, there must be an explanatory property that sets some causes apart from others. Second, the property identified must be one that is recognized by biologists as relevant to their domain(s) of inquiry. I argue that both fall short of meeting the second condition. I demonstrate this by showing how many of the biological technologies crucial to experimentation do not fit either view very well. I offer a more adequate proposal that accommodates non-actual and artificial causal variables. A consequence of my view is the following: When analyzing the causal selection practices of biologists, philosophers should consider the explanatory targets relevant to a research program – including ones whose explanans must appeal to biological technologies. I then explain how this proposal can inform the existing debate between Weber (2017) and Griffiths et al. (2015). (shrink)

The vision of natural kinds that is most common in the modern philosophy of biology, particularly with respect to the question whether species and other taxa are natural kinds, is based on a revision of the notion by Mill in A System of Logic. However, there was another conception that Whewell had previously captured well, which taxonomists have always employed, of kinds as being types that need not have necessary and sufficient characters and properties, or essences. These competing views employ (...) different approaches to scientific methodologies: Mill’s class-kinds are not formed by induction but by deduction, while Whewell’s type-kinds are inductive. More recently, phylogenetic kinds (clades, or monophyletic-kinds) are inductively projectible, and escape Mill’s strictures. Mill’s version represents a shift in the notions of kinds from the biological to the physical sciences. (shrink)

In this chapter we examine the relationship between biological information, the key biological concept of specificity, and recent philosophical work on causation. We begin by showing how talk of information in the molecular biosciences grew out of efforts to understand the sources of biological specificity. We then introduce the idea of ‘causal specificity’ from recent work on causation in philosophy, and our own, information theoretic measure of causal specificity. Biological specificity, we argue, is simple the causal (...) specificity of certain biological processes. This, we suggest, means that causal relationships in biology are ‘informational’ relationships simply when they are highly specific relationships. Biological information can be identified with the storage, transmission and exercise of biological specificity. It has been argued that causal relationships should not be regarded as informational relationship unless they are ‘arbitrary’. We argue that, whilst arbitrariness is an important feature of many causal relationships in living systems, it should not be used in this way to delimit biological information. Finally, we argue that biological specificity, and hence biological information, is not confined to nucleic acids but distributed among a wide range of entities and processes. (shrink)

A strong motivation for the human genome project was to relate biological features to the structure and function of small sets of genes, and ideally to individual genes. However, it is now increasingly realized that many problems require a "systems" approach emphasizing the interplay of large numbers of genes, and the involvement of complex networks of gene regulation. This implies a new emphasis on integrative, systems theoretical approaches. It may be called 'holistic' if the term is used without irrational (...) overtones, in the general sense of directing attention to integrated features of organs and organisms. In the history of biology, seemingly conflicting reductionist and holistic notions have alternated, with bottom-up as well as top-down approaches eventually contributing to the solutions of basic problems. By now, there is no doubt that biological features and phenomena are rooted in physico-chemical processes of the molecules involved; and yet, integrated systems aspects are becoming more and more relevant in developmental biology, brain and behavioural science, and socio-biology. -/- . (shrink)

How does evolutionary biology fit with Thomas Kuhn's famous distinction between puzzle solving and paradigm shifts in science?

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)

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)

It should now be recognized that codes are central to life and to understanding its more complex forms, including human culture. Recognizing the ‘conventional’ nature of codes provides solid grounds for rejecting efforts to reduce life to biochemistry and justifies according a place to semantics in life. The question I want to consider is whether this is enough. Focussing on Eigen’s paradox of how a complex code could originate, I will argue that along with Barbieri’s efforts to account for the (...) origins of life based on the ribosome and then to account for the refined codes through a process of ambiguity reduction, something more is required. Barbieri has not provided an adequate account of emergence, or the basis for providing such an account. I will argue that Stanley Salthe has clarified to some extent the nature of emergence by conceptualizing it as the interpolation of new enabling constraints. Clearly, codes can be seen as enabling constraints. How this actually happens, though, is still not explained. Stuart Kauffman has grappled with this issue and shown that it radically challenges the assumptions of mainstream science going back to Newton. He has attempted to reintroduce real possibilities or potentialities into his ontology, and argued that radically new developments in nature are associated with realizing adjacent possibles. This is still not adequate. What is also involved, I will suggest, utilizing concepts developed by the French natural philosopher Gilbert Simondon, is ‘transduction’ as part of ‘ontogenesis’ of individuals in a process of ‘individuation’, that is, the emergence of ‘individuals’ from preindividual fields or milieux. (shrink)

One of the central aims of science is explanation: scientists seek to uncover why things happen the way they do. This chapter addresses what kinds of explanations are formulated in biology, how explanatory aims influence other features of the field of biology, and the implications of all of this for biology education. Philosophical treatments of scientific explanation have been both complicated and enriched by attention to explanatory strategies in biology. Most basically, whereas traditional philosophy of science based explanation on derivation (...) from scientific laws, there are many biological explanations in which laws play little or no role. Instead, the field of biology is a natural place to turn for support for the idea that causal information is explanatory. Biology has also been used to motivate mechanistic accounts of explanation, as well as criticisms of that approach. Ultimately, the most pressing issue about explanation in biology may be how to account for the wide range of explanatory styles encountered in the field. This issue is crucial, for the aims of biological explanation influence a variety of other features of the field of biology. Explanatory aims account for the continued neglect of some central causal factors, a neglect that would otherwise be mysterious. This is linked to the persistent use of models like evolutionary game theory and population genetic models, models that are simplified to the point of unreality. These explanatory aims also offer a way to interpret many biologists’ total commitment to one or another methodological approach, and the intense disagreements that result. In my view, such debates are better understood as arising not from different theoretical commitments, but commitments to different explanatory projects. Biology education would thus be enriched by attending to approaches to biological explanation, as well as the unexpected ways that these explanatory aims influence other features of biology. I suggest five lessons for teaching about explanation in biology that follow from the considerations of this chapter. (shrink)

Probably the most distinctive feature of synthetic biology is its being “synthetic” in some sense or another. For some, synthesis plays a unique role in the production of knowledge that is most distinct from that played by analysis: it is claimed to deliver knowledge that would otherwise not be attained. In this contribution, my aim is to explore how synthetic biology delivers knowledge via synthesis, and to assess the extent to which this knowledge is distinctly synthetic. On the basis of (...) distinctions between knowledge-how and knowledge-why, and between syntheses that succeed and syntheses that fail, I argue that the contribution of synthesis to knowledge is best understood when syntheses are construed as experimental interventions that aim at probing causal relationships between properties of the entities that are combined through these syntheses and properties of their target products. The distinctiveness of synthetic biology in its quest for knowledge through synthesis stems from its ability to sample at will a space of empirical possibilities that is not only huge but also that has been so scarcely sampled by nature. (shrink)

Synthetic biology aims to synthesize novel biological systems or redesign existing ones. The field has raised numerous philosophical questions, but most especially what is novel to this field. In this article I argue for a novel take, since the dominant ways to understand synthetic biology’s specificity each face problems. Inspired by the examination of the work of a number of chemists, I argue that synthetic biology differentiates itself by a new regime of articulation, i.e. a new way of articulating (...) the questions and phenomena it wants to address. Instead of describing actual existing biological systems, the field aims to describe biological possibilities. In the second part I corroborate this hypothesis through a comparison between early research in the field of the origins of life and contemporary synthetic biologists, who are not so much interested in the historical origin of life on Earth, but rather in a universal biology of the possible origins of any life whatsoever. (shrink)

A minimal essentialism (‘intrinsic biological essentialism’) about natural kinds is required to explain the projectability of human science terms. Human classifications that yield robust and ampliative projectable inferences refer to biological kinds. I articulate this argument with reference to an intrinsic essentialist account of HPC kinds. This account implies that human sciences (e.g., medicine, psychiatry) that aim to formulate predictive kind categories should classify biological kinds. Issues concerning psychiatric classification and pluralism are examined.

Culture or Biology? The question can seem deep and important. Yet, I argue in this chapter, if you are enthralled by questions about our biological differences, then you are probably confused. My goal is to diagnose the confusion. In debates about the role of biology in the social world it is easy to ask the wrong questions, and it is easy to misinterpret the scientific research. We are intuitively attracted to what is called psychological essentialism, and therefore interpret what (...) is biological as what can be traced to “essences”. On this interpretation, it would be deep and important to know what about, say, the differences between the genders is biological: it would correspond to what is essential to being a man or being a woman, and be opposed to what is a mere accidental feature that some women or some men have. Yet, the psychological essentialist understanding of ‘biological differences’ is deeply mistaken about biology. It has the wrong conception of biological kinds, of biological heritability, and of how genes and hormones work. Those who argue for an important role of ‘biology’ in the explanation of human differences often see ‘the science’ on their side. But this is false – on the interpretation of ‘biological differences’ that is most intuitive and that makes the question appear to be most interesting. Defenders of ‘biology’ often have the science against them. What is often called ‘biology’ is a myth: a myth created by an intuitive tendency that grotesquely distorts real biological research. (shrink)

Chapter 1st of the book. This chapter explores the fundamental ambiguity of the concept of plasticity – between openness and determination, change and stabilization of forms. This pluralism of meanings is used to unpack different instantiations of corporeal plasticity across various epochs, starting from ancient and early modern medicine, particularly humouralism. A genealogical approach displaces the notion that plasticity is a unitary phenomenon, coming in the abstract, and illuminates the unequal distribution of different forms of plasticities across social, gender, and (...) ethnic groups. Taking a longer view of the plastic body as a ubiquitous belief in traditions predating and coexisting with modern medicine will help contextualize the seeming radicalism of today’s turn to permeability and the exceptionalism of Western findings. By highlighting the complex biopolitical usages of plasticity in the past, the chapter warns against simplistic appropriations of the term in contemporary body/world configurations driven by findings in neuroscience, epigenetics and microbiomics. (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)

Much has been made of how Darwinian thinking destroyed proofs for the existence of God from ‘design’ in the universe. I challenge that prevailing view by looking closely at classical ‘teleological’ arguments for the existence of God. One version championed by Aristotle and Thomas Aquinas stems from how chance is not a sufficient kind of ultimate explanation of the universe. In the course of constructing this argument, I argue that the classical understanding of teleology is no less necessary in modern (...) Darwinian biology than it was in Aristotle's time. In fact, modern biology strengthens the claims that teleological arguments make by vindicating many of their key features. As a consequence, I show how Aristotle and Aquinas' teleological argument for an intelligent First Cause remains valid. (shrink)

Common sense morality and legislations around the world ascribe normative relevance to biological connections between parents and children. Procreators who meet a modest standard of parental competence are believed to have a right to rear the children they brought into the world. I explore various attempts to justify this belief and find most of these attempts lacking. I distinguish between two kinds of biological connections between parents and children: the genetic link and the gestational link. I argue that (...) the second can better justify a right to rear. (shrink)

Some moral realists claim that moral facts are a species of natural fact, amenable to scientific investigation. They argue that these moral facts are needed in the best explanations of certain phenomena and that this is evidence that they are real. In this paper I present part of a biological account of the function of morality. The account allows the identification of a plausible natural kind that could play the explanatory role that a moral kind would play in naturalist (...) realist theories. It is therefore a candidate for being the moral kind. I argue, however, that it will underdetermine the morally good, that is, identifying the kind is not sufficient to identify what is good. Hence this is not a natural moral kind. Its explanatory usefulness, however, means that we do not have to postulate any further (moral) facts to provide moral explanations. Hence there is no reason to believe that there are any natural moral kinds. (shrink)

Biological theory demands a clear organism concept, but at present biologists cannot agree on one. They know that counting particular units, and not counting others, allows them to generate explanatory and predictive descriptions of evolutionary processes. Yet they lack a unified theory telling them which units to count. In this paper, I offer a novel account of biological individuality, which reconciles conflicting definitions of ‘organism’ by interpreting them as describing alternative realisers of a common functional role, and then (...) defines individual organisms as essentially possessing some mechanisms that play this role. (shrink)

Background: how mind functions is subject to continuing scientific discussion. A simplistic approach says that, since no convincing way has been found to model subjective experience, mind cannot exist. A second holds that, since mind cannot be described by classical physics, it must be described by quantum physics. Another perspective concerns mind's hypothesized ability to interact with the world of quanta: it should be responsible for reduction of quantum wave packets; physics producing 'Objective Reduction' is postulated to form the basis (...) for mind-matter interactions. This presentation describes results derived from a new approach to these problems. It is based on well-established biology involving physics not previously applied to the fields of mind, or consciousness studies, that of critical feedback instability. -/- Methods: 'self-organized criticality' in complexity biology places system loci of control at critical instabilities, physical properties of which, including information properties, are presented. Their elucidation shows that they can model hitherto unexplained properties of experience. -/- Results: All results depend on physical properties of critical instabilities. First, at least one feed-back or feed-forward loop must have feedback gain, g = 1: information flows round the loop impress perfect images of system states back on themselves: they represent processes of perfect self-observation. This annihilates system quanta: system excitations are instability fluctuations, which cannot be quantized. Major results follow: -/- 1. Information vectors representing criticality states must include at least one attached information loop denoting self-observation. -/- 2. Such loop structures are attributed a function, 'registering the state's own existence', explaining -/- a. Subjective 'awareness of one's own presence' -/- b. How content-free states of awareness can be remembered (Jon Shear) -/- c. Subjective experience of time duration (Immanuel Kant) -/- d. The 'witness' property of experience – often mentioned by athletes 'in the zone' -/- e. The natural association between consciousness and intelligence -/- This novel, physically and biologically sound approach seems to satisfactorily model subjectivity. -/- Further significant results follow: -/- 1. Registration of external information in excited states of systems at criticality reduces external wave-packets: the new model exhibits 'Objective Reduction' of wave packets. -/- 2. High internal coherence (postulated by Domash & Penrose) leading to a. Non-separable information vector bundles. b. Non-reductive states (Chalmers's criterion for experience). -/- 3. Information that is: a. encoded in coherence negentropy; b. non-digitizable, and therefore c. computationally without digital equivalent (posited by Penrose). -/- Discussion and Conclusions: instability physics implies anharmonic motion, preventing excitation quantization, and totally different from the quantum physics of simple harmonic motion at stability. Instability excitations are different from anything hitherto conceived in information science. They can model aspects of mind never previously treated, including genuine subjectivity, objective reduction of wave-packets, and inter alia all properties given above. (shrink)

The paper examines the relationship between the biological and the social in morals. Its conclusion is that the biological is one among other sources of moarls. The social developed as another, much more dynamic source. An important role is played by free will or the moral freedom, especially on the individual morals level. It is the consequences, and especially social consequences, that in the author's viewpoint to the actual state of social and individual morals.