John Dupré explores recent revolutionary developments in biology and considers their relevance for our understanding of human nature and human society. Epigenetics and related areas of molecular biology have eroded the exceptional status of the gene and presented the genome as fully interactive with the rest of the cell. Developmental systems theory provides a space for a vision of evolution that takes full account of the fundamental importance of developmental processes. Dupré shows the importance of microbiology for a (...) proper understanding of the living world, and reveals how it subverts such basic biological assumptions as the organisation of biological kinds on a branching tree of life, and the simple traditional conception of the biological organism. (shrink)

In recent years, an increasing number of theoretical biologists and philosophers of biology have been opposing reductionist research agendas by appealing to the concept of biological autonomy which draws on the older concept of autopoiesis. In my paper, I investigate some of the ontological implications of this approach. The emphasis on autonomy and autopoiesis, together with the associated idea of organisational closure, might evoke the impression that organisms are to be categorised ontologically as substances: ontologically independent, well-individuated, discrete particulars. (...) However, I argue that this is mistaken. Autopoiesis and biological autonomy, properly understood, require a rigorous commitment to a process ontological view of life. (shrink)

John Dupr explores recent revolutionary developments in biology and considers their relevance for our understanding of human nature and society. He reveals how the advance of genetic science is changing our view of the constituents of life, and shows how an understanding of microbiology will overturn standard assumptions about the living world.

Biological processes are often explained by identifying the underlying mechanisms that generate a phenomenon of interest. I characterize a basic account of mechanistic explanation and then present three challenges to this account, illustrated with examples from molecular biology. The basic mechanistic account is insufficient for explaining nonsequential and nonlinear dynamic processes, is insufficient for explaining the inherently stochastic nature of many biological mechanisms, and fails to give a proper framework for analyzing organization. I suggest that biological processes are best (...) approached as a multidimensional gradient—with some processes being paradigmatic cases of mechanisms and some being marginal cases. (shrink)

In his famous essentialist account of identity, Kripke holds that it is necessary to the identity of individual people that they have the parents they do in fact have. Some have disputed this requirement, treating it either as a reason to reject essentialism or as something that should be eliminated in order to make essentialism stronger. I examine the reasoning behind some of these claims and argue that it fails to acknowledge the complex and multi-faceted importance of biological process (...) in determining identity and distinguishing significant differences between biological and non-biological cases. In fact, this failure derives from an inherent tendency to treat the biological case in just the same way as the non-biological case at least at one important point in its history—the point of formation. This analysis offers a way of salvaging Kripke’s original claims. I focus in particular on the views of Graeme Forbes and Teresa Robertson, but also discuss the views of Nathan Salmon, M. S. Price and E. J. Lowe. (shrink)

In recent years, an increasing number of theoretical biologists and philosophers of biology have been opposing reductionist research agendas by appealing to the concept of biological autonomy which draws on the older concept of autopoiesis. In my paper, I investigate some of the ontological implications of this approach. The emphasis on autonomy and autopoiesis, together with the associated idea of organisational closure, might evoke the impression that organisms are to be categorised ontologically as substances: ontologically independent, well-individuated, discrete particulars. (...) However, I argue that this is mistaken. Autopoiesis and biological autonomy, properly understood, require a rigorous commitment to a process ontological view of life. (shrink)

The key assumption behind evolutionary epistemology is that animals are active learners or ‘knowers’. In the present study, I updated the concept of natural learning, developed by Henry Plotkin and John Odling-Smee, by expanding it from the animal-only territory to the biosphere-as-a-whole territory. In the new interpretation of natural learning the concept of biological information, guided by Peter Corning’s concept of “control information”, becomes the ‘glue’ holding the organism–environment interactions together. The control information guides biological systems, from bacteria to ecosystems, (...) in the process of natural learning executed by the universal algorithm. This algorithm, summarized by the acronym IGPT (information-gain-process-translate) incorporates natural cognitive methods including sensing/perception, memory, communication, and decision-making. Finally, the biosphere becomes the distributed network of communicative interactions between biological systems termed the interactome. The concept of interactome is based on Gregory Bateson’s natural epistemology known as the “ecology of mind”. Mimicking Bateson’s approach, the interactome may also be designated “physiology of mind”—the principle behind regulating the biosphere homeostasis. (shrink)

Human persons exist longer than a single moment in time; they persist through time. However, so far it has not been possible to make this natural and widespread assumption metaphysically comprehensible. The philosophical debate on personal identity is rather stuck in a dilemma: reductionist theories explain personal identity away, while non-reductionist theories fail to give any informative account at all. This chapter argues that this dilemma emerges from an underlying commitment, shared by both sides of in the debate, to an (...) ontology which that gives the priority to static unchanging things. The claim defended here is that the dilemma of personal identity can be overcome if we acknowledge the biological nature of human persons and switch to a process- ontological framework that takes process and change to be ontologically primary. Human persons are biological higher-order processes, rather than things, and their identity conditions can be scientifically investigated. (shrink)

The theoretical biology movement originating in Britain in the early 1930’s and the biosemiotics movement which took off in Europe in the 1980’s have much in common. They are both committed to replacing the neo-Darwinian synthesis, and they have both invoked theories of signs to this end. Yet, while there has been some mutual appreciation and influence, particularly in the cases of Howard Pattee, René Thom, Kalevi Kull, Anton Markoš and Stuart Kauffman, for the most part, these movements have (...) developed independently of each other. Focussing on morphogenesis understood as vegetative semiosis, in this paper I will argue that the ideas of these movements are commensurate. Furthermore, synthesising them would enable us to see life processes as proto-narratives. Doing so will involve synthesising biohermeneutics, Peircian biosemiotics with Waddington’s theoretical biology and Piagetian genetic structuralism, and this, I claim, would strengthen the challenge of these traditions to mainstream biology. At the same time, this should contribute to overcoming the opposition between the sciences and the humanities, developing a broader tradition of Schellingian thought which involves developing the humanities and then demanding of the physical and biological sciences that they are consistent with and can make intelligible the emergence of humans as conceived by the humanities. (shrink)

Biological motion is the phenomenon of recognizing a human form out of moving point-light dots, where both bottom–up and top–down processing mechanisms have been reported. This study reviews available psychological and neuroscientific evidence, and it assesses attempts either to assimilate biological motion to other structure-from-motion cases or to include biological motion into a visual “social cognition” subsystem . While neither theoretical option seems to accommodate all relevant psychological results, the study proposes that biological motion may be an object recognition task, (...) inside the framework of Pylyshyn’s sequence of data-driven and cognitive mechanisms. This implies that a bottom–up object construction out of two-dimensional stimulus information precedes a top–down, but emotionally significant categorization of a particular human movement. Recognition of biological motion may be an example of visual processing in general. (shrink)

Probability and indeterminism have always been core philosophical themes. This paper aims to contribute to understanding probability and indeterminism in biology. To provide the background for the paper, it will first be argued that an omniscient being would not need the probabilities of evolutionary theory to make predictions about biological processes. However, despite this, one can still be a realist about evolutionary theory, and then the probabilities in evolutionary theory refer to real features of the world. This prompts the (...) question of how to interpret biological probabilities which correspond to real features of the world but are in principle dispensable for predictive purposes. This paper will suggest three possible interpretations. The first interpretation is a propensity interpretation of kinds of systems. It will be argued that backward probabilities in biology do not present a problem for this propensity interpretation. The second interpretation is the frequency interpretation. Third, I will suggest Humean chances are a new interpretation of probability in evolutionary theory. Finally, this paper discusses Sansom’s argument that biological processes are indeterministic because probabilities in evolutionary theory refer to real features of the world. It will be argued that Sansom’s argument is not conclusive, and that the question whether biological processes are deterministic or indeterministic is still with us. (shrink)

(1997). Information processing as an intrinsic property of biological systems: Origin and dynamics of information. World Futures: Vol. 50, No. 1-4, pp. 571-581.

The aim of this book is to show how supramolecular complexity of cell organization can dramatically alter the functions of individual macromolecules within a cell. The emergence of new functions which appear as a consequence of supramolecular complexity, is explained in terms of physical chemistry. The book is interdisciplinary, at the border between cell biochemistry, physics and physical chemistry. This interdisciplinarity does not result in the use of physical techniques but from the use of physical concepts to study biological problems. (...) In the domain of complexity studies, most works are purely theoretical or based on computer simulation. The present book is partly theoretical, partly experimental and theory is always based on experimental results. Moreover, the book encompasses in a unified manner the dynamic aspects of many different biological fields ranging from dynamics to pattern emergence in a young embryo. The volume puts emphasis on dynamic physical studies of biological events. It also develops, in a unified perspective, this new interdisciplinary approach of various important problems of cell biology and chemistry, ranging from enzyme dynamics to pattern formation during embryo development, thus paving the way to what may become a central issue of future biology. (shrink)

In this paper, I propose a theory of living organisms that captures the insights of both traditional Aristotelian hylomorphism and John Dupré's “biological processualism”. Like traditional Aristotelian hylomorphism, the proposed theory understands material objects to be comprised of both matter and form. Unlike contemporary structural varieties of hylomorphism, however, it does not understand the form of a material object to be a relation, configuration, or structure exhibited by its parts but an activity or process in which its matter is (...) continuously engaged. Following Mark Steen, I call the proposed theory “Hyloenergeism”. As a version of hylomorphism, hyloenergeism better captures the inherent dynamism of living organisms than contemporary structural approaches. And it does so not by abandoning the substantialist paradigm, as Dupré's biological processualism does, but by reconceptualizing the nature of material substances as possessing a processual core. Hyloenergeism, then, paves a middle way for those looking for a substance view of living organisms sensitive to the concerns raised by contemporary processualist philosophers of biology. (shrink)

For most philosophers of psychology and cognitive science, inquiry into human cognitive activity begins at the level of intrapersonal processes. A central question is whether these processes are sufficiently autonomous from more basic neurophysiological processes to be investigated in their own terms, or whether all explanations must be in neurophysiological terms. Some philosophers have insisted on the relative autonomy of the cognitive level. One currently quite popular view, eliminative materialism, however, holds that the explanations that have been advanced at the (...) intrapersonal cognitive level are misguided, and must be replaced by accounts developed from an understanding of the underlying neurophysiological processes. (shrink)

In spite of being ubiquitous in life sciences, the concept of information is harshly criticized. Uses of the concept other than those derived from Shannon's theory are denounced as pernicious metaphors. We perform a computational experiment to explore whether Shannon's information is adequate to describe the uses of said concept in commonplace scientific practice. Our results show that semantic sequences do not have unique complexity values different from the value of meaningless sequences. This result suggests that quantitative theoretical frameworks do (...) not account fully for the complex phenomenon that the term “information” refers to. We propose a restructuring of the concept into two related, but independent notions, and conclude that a complete theory of biological information must account completely not only for both notions, but also for the relationship between them. (shrink)

Comparative biology builds up systematic knowledge of the diversity of life, across evolutionary lineages and levels of organization, starting with evidence from a sparse sample of model organisms. In developmental biology, a key obstacle to the growth of comparative approaches is that the concept of homology is not very well defined for levels of organization that are intermediate between individual genes and morphological characters. In this paper, we investigate what it means for ontogenetic processes to be homologous, focusing (...) specifically on the examples of insect segmentation and vertebrate somitogenesis. These processes can be homologous without homology of the underlying genes or gene networks, since the latter can diverge over evolutionary time, while the dynamics of the process remain the same. Ontogenetic processes like these therefore constitute a dissociable level and distinctive unit of comparison requiring their own specific criteria of homology. In addition, such processes are typically complex and nonlinear, such that their rigorous description and comparison not only requires observation and experimentation, but also dynamical modeling. We propose six criteria of process homology, combining recognized indicators with novel ones derived from dynamical systems modeling. We show how these criteria apply to animal segmentation and other ontogenetic processes. We conclude by situating our proposed dynamical framework for homology of process in relation to similar research programs, such as process structuralism and developmental approaches to morphological homology. (shrink)

It is often argued that the continuity of the processes of embryo development precludes the establishment of morally significant boundaries, once development is under way. These arguments typically claim that marking out any moral boundaries requires identifying particular significant events, and that in such circumstances this is either impossible or arbitrary. In this paper it is argued that arguments of this kind are not cogent. The paper concludes by indicating where the real problems lie.

Despite wide acceptance that the attributes of living creatures have appeared through a cumulative evolutionary process guided chiefly by natural selection, many human activities have seemed analytically inaccessible through such an approach. Prominent evolutionary biologists, for example, have described morality as contrary to the direction of biological evolution, and moral philosophers rarely regard evolution as relevant to their discussions. -/- The Biology of Moral Systems adopts the position that moral questions arise out of conflicts of interest, and that (...) moral systems are ways of using confluences of interest at lower levels of social organiation to deal with conflicts of interest at higher levels. Moral systems are described as systems of indirect reciprocity: humans gain and lose socially and reproductively not only by direct transactions, but also by the reputations they gain from the everyday flow of social interactions. -/- The author develops a general theory of human interests, using senescence and effort theory from biology, to help analye the patterning of human lifetimes. He argues that the ultimate interests of humans are reproductive, and that the concept of morality has arisen within groups because of its contribution to unity in the context, ultimately, of success in intergroup competition. He contends that morality is not easily relatable to universals, and he carries this argument into a discussion of what he calls the greatest of all moral problems, the nuclear arms race. (shrink)

Biologists increasingly report anthropogenic disruptions of both organisms and ecosystems, suggesting that these processes are a fundamental, qualitative component of the Anthropocene. Nonetheless, the notion of disruption has not yet been theorized in biology. To progress in that regard, we work on a special case. Relatively minor temperature changes impact plant-pollinator synchrony, disrupting mutualistic interaction networks. Understanding this phenomenon requires a specific rationale since models describing them use both historical and systemic reasoning. Specifically, history justifies that the system is (...) initially in a very narrow part of the possibility space where it is viable, and the disruption randomizes this configuration. Building on this rationale, we develop a formal framework inspired by Boltzmann's entropy. With empirical networks, we show historical trends depending on latitude. Then we propose an initial definition of disruption in ecology. When a specific historical outcome contributes to a system's viability, disruption randomizes this outcome, decreasing viability. (shrink)

In this volume, Andrea Borghini and Elena Casetta introduce a wide spectrum of key philosophical problems related to life sciences in a neat framework and an accessible style, with a special emphasis on metaphysical issues. The volume is divided into three parts. The first addresses the two main questions stemming from life sciences: what is life, and what is the correct understanding of the theory of evolution? The second part looks at metaphysical questions concerning biological entities: environments, species, organisms, and (...) biological individuals. The third part focuses on theoretical questions of particular ethical and political significance: sex and gender, the biotechnological revolution, and the evolution of behavior and culture. Each chapter is followed by a list of further readings. (shrink)

A crucial question for a process view of life is how to identify a process and how to follow it through time. The genidentity view can contribute decisively to this project. It says that the identity through time of an entity X is given by a well-identified series of continuous states of affairs. Genidentity helps address the problem of diachronic identity in the living world. This chapter describes the centrality of the concept of genidentity for David Hull and (...) proposes an extension of Hull’s view to the ubiquitous phenomenon of symbiosis. Finally, using immunology as a key example, it shows that the genidentity view suggests that the main interest of a process approach is epistemological rather than ontological and that its principal claim is one of priority, namely that processes precede and define things, and not vice versa. (shrink)

When a group of processes achieves such closure that a set of states of affairs recurs continually, then the effect of that coherence on the world differs from what would occur in the absence of that closure. Such altered effectiveness is an attribute of the system as a whole, and would have consequences. This indicates that the network of processes, as a unit, has ontological significance. Whenever a network of processes generates continual return to a limited set of states of (...) affairs, the system may function as a “whole”— with respect to appropriate interaction partners. The balance achieved by the processes provides the form of definiteness of a unified agent. The causal powers of such coherent aggregates are indeed just the powers of the “constituents acting in concert”. However, the components act in concert in the specific way they do only because of their inclusion in the closed set of interactions that defines the coherence. This renders the causal powers of the coherence defined by that closure non-redundant, and hence the coherence, as a unit, is ontologically significant. The form of definiteness that provides internal coherence also grounds external efficacy of the societal aggregation. The closure is a structural feature of the coherence — possibly, but not necessarily, apparent in spatial structuring. This approach can provide a unified account that includes quantum microphysics, systems biology, and the philosophy of organism ─ without reducing any of these to another. (shrink)

Universal ranks in folk biological taxonomy probably apply to taxonomies of cultural artifacts. We cannot call folk biological cognition domain-specific and modular. Color categorization may manifest unique organization, which would result from known neurology and the nature of color as an attribute. But folk biology does not adduce equivalent evidence. A global process of increasing differentiation similarly affects folk taxonomy, color categorization, and other practices germane to Atran's anthropology of science; this is beclouded by claims of specificity and (...) modularity. (shrink)

Science and religion contend for the world's allegiance. Scientists are bewildered by people's acceptance of some seemingly irrational values and judgments endorsed by religion. They argue strenuously with people about the common good and systemic consequences of actions, but are trumped by religious nostrums. Why? Science and religion both arise from our bewilderment with the complexity of our lives. At their roots they are vital, necessary, liberating, and complementary processes. So, why the perceived conflict? Experiences of universal unity arise naturally (...) in deep meditative states. What does this recently demonstrated biological fact tell us about our tendencies to religious belief? (shrink)

The purpose of the study was to compare the visuospatial decision-making error scores related to the perception of biological motion of individuals categorized as field dependent or field independent. A sample of 69 participants aged 18-27 years that included 33 males and 36 females completed the experiment. Cognitive style was assessed using the Group Embedded Figure Test. Perception of biological motion was evaluated using two different point-light stimuli developed from video images of a ballet dancer’s performance of a correct and (...) incorrect turn in the fifth position. The results showed that individuals classified as field independent made significantly fewer visuospatial processing errors. The findings are considered and discussed in relation to theoretical perspectives associated with both cognitive processing and cognitive style. (shrink)

CRAN R code to analyze disruption of plant-pollinator networks for the article: Disruption of biological processes in the Anthropocene: the case of phenological mismatch Cite as Montévil, M. 2020, code for: Disruption of biological processes in the Anthropocene: the case of phenological mismatch DOI: 10.5281/zenodo.4290412.

Remapping Biology with Goethe, Schelling, and Herder recruits a Romantic philosophy of biology into contemporary debates to both integrate the theoretical implications of ecology, evolution, and development, and to contextualize the successes of the Modern Evolutionary Synthesis's gene's-eye-view of biology. The dominant philosophy of biology in the twentieth century was one developed within and for the Modern Evolutionary Synthesis. As biologists like those developing an Extended Evolutionary Synthesis have pushed the limits of this paradigm, fresh philosophical (...) approaches have become necessary. This book makes the case that an organicism developed by the 19th century figures Goethe, Schelling, and Herder offers surprising resources to navigate the contemporary biological and evolutionary terrain. This "metamorphic organicism" resonates with present trends in biological theory that emphasize process, organismal dynamics, ecology, and agency. It also proposes strategies for reintegrating reductive and mechanistic maps of biology, like those of the Modern Evolutionary Synthesis, into richer theoretical representations of life. Drawing from cutting-edge biology, Romantic history, and perspectival pluralist literatures, this integrated history-and-philosophy-of-biology will be of interest to students and scholars interested in the genesis of current theoretical tensions in evolutionary biology, and to those seeking constructive ways to resolve those tensions, including practicing biologists and educators. (shrink)

Justin Garson has recently argued that proper functions are proximal activities of traits selected by phylogenetic or ontogenetic selection processes, and that traits are dysfunctional only if they cannot perform their proper functions for constitutional reasons. We partially agree with Garson, but reject the view that functions are proximal activities, as well as his account of dysfunctions. Instead, we propose our own theory that biological functions are selected dispositions and that a trait is dysfunctional in virtue of not having the (...) dispositions for which it was selected. This account can explain both defects (or dysfunctions in Garson’s sense) and dysfunctions due to environmental factors. Moreover, it offers a neat way to explain the graduality of dysfunction. (shrink)

Recently something close to a consensus about the best way to naturalize the notion of biological function appears to be emerging. Nonetheless, teleological notions in biology remain controversial. In this paper we provide a naturalistic analysis for the notion of natural design. Many authors assume that natural design should be assimilated directly to function. Others find the notion problematic because it suggests that evolution is a directed process. We argue that both of these views are mistaken. Our naturalistic (...) account does not simply equate design with function. We argue that the distinction between function and design is important for understanding the evolution of the physical and behavioral traits of organisms. (shrink)

I offer a defense, albeit a qualified one, of machine analogies in biology, focusing on molecular contexts. The defense is rooted in my prior work (Levy in Philosopher’s Imprint 14(6), 2014), which construes the machine machine-likeness of a system as a matter of the extent to which it exhibits an internal division of labor. A concrete aim is to shore up the notion of molecular biological machines, paying special attention to processive molecular motors, such as Kinesin. But I will (...) also try to show how the division of labor account gives us guidance more broadly, both about where and why machine analogies can be expected to prove helpful and about their limitations. (shrink)

“Biological Naturalism” is a name I have given to an approach to what is traditionally called the mind-body problem. The way I arrived at it is typical of the way I work: try to forget about the philosophical history of a problem and remind yourself of what you know for a fact. Any philosophical theory has to be consistent with the facts. Of course, something we think is a fact may turn out not to be, but we have to start (...) with our best information. Biological Naturalism is a theory of mental states in general but as this book is about consciousness I will present it here as a theory of consciousness. (shrink)

I give a biological account of epistemic normativity. My account explains the sense in which it is true that belief is subject to a standard of correctness, and reduces epistemic norms to there being doxastic strategies which guide how best to meet that standard. Additionally, I give an explanation of the mistakes we make in our epistemic discourse, understood as either taking epistemic properties and norms to be sui generis and irreducible, and/or as failing to recognize the reductive base of (...) epistemic normativity. This explanation will appeal to the claim that the beliefs which constitute our epistemic discourse are false but adaptive, and are the outcome of a non-truth tracking process. The opponents of my position are philosophers who take epistemic normativity not to be reducible in this way, and to involve sui generis properties and norms governing belief. The aim of the paper is to show that epistemic normativity can be explained by appeal to the biological functions of our mechanisms of belief-production. (shrink)

Deweyan pedagogy seeks to promotes growth, characterized as an increased sensitivity, responsiveness, and ability to participate in an environment. Growth, Dewey says, is fostered by the development of habits that enable further habit formation. Unfortunately, humans have their own habitual ways of encountering other species, which often do not support growth. In this article, I briefly review some common conceptions of learning and the process of habit-formation to scope out the landscape of a more responsible and responsive approach to (...) taking growth seriously. What emerges is a reflexive biosemiotics that has humans explicitly concerned with the in situ emergence of new signification in themselves and in other organisms. This requires we take a pedagogical stance in our attitudes and practices towards other species, which we can enrich with insights derived from re-interpreting traditional empirical studies. By freeing the habit-forming process from confining stereotype, a biological pedagogy can enable a more fluid and creative biosphere, unencumbered to explore unfolding possibilities in semiotic space. (shrink)

This commentary focuses on the importance of auditory object processing for producing and comprehending human language, the relative lack of development of this capability in nonhuman primates, and the consequent need for hominid neurobiological evolution to enhance this capability in making the transition from protosign to protospeech to language.

The concept of genidentity has been proposed as a way to better understand identity through time, especially in physics and biology. The genidentity view is utterly anti-substantialist in so far as it suggests that the identity of X through time does not presuppose whatsoever the existence of a permanent “core” or “substrate” of X. Yet applications of this concept to real science have been scarce and unsatisfying. In this paper, our aim is to show that a well-defined concept of (...) functional genidentity can be crucial to shed light on identity through time in classical physics and especially in biology. Finally, we show that understanding identity on the basis of continuity suggests a move towards an ontology of processes. (shrink)

Developmental biology is the science that investigates how a variety of interacting processes generate an organism’s heterogeneous shapes, size, and structural features that arise on the trajectory from embryo to adult, or more generally throughout a life cycle. It represents an exemplary area of contemporary experimental biology that focuses on phenomena that have puzzled natural philosophers and scientists for more than two millennia. Philosophers of biology have shown interest in developmental biology due to the potential relevance (...) of development for understanding evolution, the theme of reductionism in genetic explanations, and via increased attention to the details of particular research programs, such as stem cell biology. Developmental biology displays a rich array of material and conceptual practices that can be analyzed to better understand the scientific reasoning exhibited in experimental life science. This entry briefly reviews some central phenomena of ontogeny and then explores four domains that represent some of the import and promise of conceptual reflection on the epistemology of developmental biology. (shrink)

Here is a universal biology that draws upon the contributions of Aristotle, Kant, and Hegel to unravel the mystery of life and conceive what is essential to living things anywhere they may arise. The book develops a philosopher’s guide to life in the universe, conceiving how nature becomes a biosphere in which life can emerge, what are the basic life processes common to any organism, how evolution can give rise to the different possible forms of life, and what distinguishes (...) the essential life forms from one another. (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)

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)