This chapter draws on insights from non-equilibrium thermodynamics to demonstrate the ontological inadequacy of the machine conception of the organism. The thermodynamic character of living systems underlies the importance of metabolism and calls for the adoption of a processual view, exemplified by the Heraclitean metaphor of the stream of life. This alternative conception is explored in its various historical formulations and the extent to which it captures the nature of living systems is examined. Following this, the chapter considers the metaphysical (...) implications of reconceptualizing the organism from complex machine to flowing stream. What do we learn when we reject the mechanical and embrace the processual? Three key lessons for biological ontology are identified. The first is that activity is a necessary condition for existence. The second is that persistence is grounded in the continuous self-maintenance of form. And the third is that order does not entail design. (shrink)

The term “origin” is associated with a beginning, a debut, a birth. Expressions such as “the origin of life” or “the origin of man” suggest unique moments linked to remarkable phenomena. In the following pages, we will attempt to show that, since its birth, the universe has been undergoing a process of self-organization. The appearance of life on Earth represents one of the stages in this process.

This paper examines a new challenge to neo-Darwinism, a movement known as process structuralism. The process structuralist critique of neo-Darwinism holds 1) that there are general laws in biology and that biologists should search for these laws; 2) that there are general forms of morphology and development and that biologists should attempt to uncover these forms; 3) that organisms are unified wholes that cannot be understood without adopting a holistic perspective; and 4) that no special, causal primacy should be given (...) to the genes in development and morphology. This paper places process structuralism in its historical context, examines the philosophical underpinnings of the movement, and discusses some of the evidence used to support its claims. (shrink)

Classifying is a fundamental operation in the acquisition of knowledge. Taxonomic theory can help students of cognition, evolutionary psychology, ethology, anatomy, and sociobiology to avoid serious mistakes, both practical and theoretical. More positively, it helps in generating hypotheses useful to a wide range of disciplines. Composite wholes, such as species and societies, are “individuals” in the logical sense, and should not be treated as if they were classes. A group of analogous features is a natural kind, but a group of (...) homologous features is not. Imposing hypotheses justified only on the basis of nominalist, realist, phenomenalist, or conceptualist metaphysics upon the neurophysiology of organisms or upon the causes of behavior exemplifies the “psychologist's fallacy” of William James. Levels should be distinguished from their members and from classes of levels, and the ontological status of entities ranked at levels should be made clear. It is important not to confuse such categories as substance and process with one another. Several genetical terms, such as “gene” and chromosome,” are even more equivocal than has been realized. Discussions about units of selection, behavior, and thinking suffer from the ambiguity of a “unit of” an entity. An important source of misunderstanding about natural selection is the habit of treating it as an “agent”: in an important sense, natural selection does not “act” at all. (shrink)

We begin at the beginning, with an outline of Aristotle’s views on ontology and with a discussion of the influence of these views on Linnaeus. We move from there to consider the data standardization initiatives launched in the 19th century, and then turn to investigate how the idea of computational ontologies developed in the AI and knowledge representation communities in the closing decades of the 20th century. We show how aspects of this idea, particularly those relating to the use of (...) the term 'concept' in ontology development, influenced SNOMED CT and other medical terminologies. Against this background we then show how the Foundational Model of Anatomy, the Gene Ontology, Basic Formal Ontology and other OBO Foundry ontologies came into existence and discuss their role in the development of contemporary biomedical informatics. (shrink)

Following Mayr (1961) evolutionary biologists often maintain that the hallmark of biology is its evolutionary perspective. In this view, biologists distinguish themselves from other natural scientists by their emphasis on why-questions. Why-questions are legitimate in biology but not in other natural sciences because of the selective character of the process by means of which living objects acquire their characteristics. For that reason, why-questions should be answered in terms of natural selection. Functional biology is seen as a reductionist science that applies (...) physics and chemistry to answer how-questions but lacks a biological point of view of its own. In this paper I dispute this image of functional biology. A close look at the kinds of issues studied in biology and at the way in which these issues are studied shows that functional biology employs a distinctive biological perspective that is not rooted in selection. This functional perspective is characterized by its concern with the requirements of the life-state and the way in which these are met. (shrink)

Massimiliano Simons provides the first systematic study of Serres' work in the context of late 20th-century French philosophy of science. By proposing new readings of Serres' philosophy, Simons creates a synthesis between his predecessors, Gaston Bachelard, Georges Canguilhem, and Louis Althusser as well as contemporary Francophone philosophers of science such as Bruno Latour and Isabelle Stengers. Simons situates Serres' unique contribution through his notion of the quasi-object, a concept, he argues, organizes great parts of Serres' work into a promising philosophy (...) of science as well as a challenge to the narrower field of French epistemology, to which it has often been limited. Simons highlights how the concept encompasses Serres' commitment to positive relations between science and culture and his rejection of pleas to purify the scientific self from imaginative and cultural elements. It helps to situate Serres between the distinct traditions of Bachelard and Latour as well as progressing the innovative aspects of Serres' philosophy for current debates in the philosophy, history, and sociology of science. Showing how Serres' philosophy can serve as a normative approach to science and technology, Michel Serres and French Philosophy of Science takes in themes of materiality, religiosity, modernity and ecology to advance a timely alternative to philosophy of science for contemporary life. (shrink)

A central thesis of intelligent‐design theorists is that physical and chemical laws and chance are insufficient to account for irreducibly complex biological structures and that intelligent design is necessary to account for such phenomena. This assertion, however, still implies a reductionist ontology. We need to recognize that reality displays multiple modes of being beyond simply chemical and physical modes of being, each of which is governed by laws for that mode of being. This essay argues for an alternate framework for (...) understanding life phenomena that is neither philosophical materialism nor intelligent‐design theory. (shrink)

partial review of Thomas Nagel’s book, Mind and Cosmos: Why the Materialist Neo-Darwinian Conception of Nature Is Almost Certainly False is used to articulate some systems-theoretic ideas about the challenge of understanding subjective experience. The article accepts Nagel’s view that reductionist materialism fails as an approach to this challenge, but argues that seeking an explanation of mind based on emergence is more plausible than seeking one based on pan-psychism, which Nagel favors. However, the article proposes something similar to Nagel’s neutral (...) monism by positing a hierarchy of information processes that spans the domains of matter, life, and mind. As depicted in this hierarchy, subjective experience is emergent, but also continuous with informational phenomena at lower levels. (shrink)

We address issues of description of the origin and evolution of the genetic code from a semiotics standpoint. Developing the concept of codepoiesis introduced by Barbieri, a new idea of semio-poiesis is proposed. Semio-poiesis, a recursive auto-referential processing of semiotic system, becomes a form of organization of the bio-world when and while notions of meaning and aiming are introduced into it. The description of the genetic code as a semiotic system allows us to apply the method of internal reconstruction to (...) it: on the basis of heterogeneity and irregularity of the current state, to explicate possible previous states and various ways of forming mechanisms of coding and textualization. The revealed patterns are consistent with hypotheses about the origin and evolution of the genetic code. (shrink)

Our environmental crisis is commonly explained as a product of a set of attitudes and beliefs about the world which have been developed by post‐Cartesian technological society. Deep ecologists claim that the crisis can only be overcome by adopting an alternative non‐technological paradigm, such as can be discovered in non‐Western cultures. In this paper I express misgivings about the use of the expression ‘Paradigm’ by deep ecologists, question the claim that a science‐based world‐view inevitably fosters manipulative and exploitative attitudes to (...) the natural world, suggest that non‐technological cultures do not necessarily provide exemplary and superior models for relating to the natural world, and defend a scientific naturalism as a satisfying way of realising our unity with the natural world. (shrink)

I will discuss some of the implications of the ongoing Darwinian revolution for theology as a constructor and interpreter of human meaning. Focus will be directed toward the following issues: How should we best understand ourselves in the new, evolutionary cosmos? What are the problems with the kind of genetic reductionism espoused by neo‐Darwinism? How are those problems resolved by the “relational” understanding of life made available by thermodynamics and ecology? How do we generate meaning‐structures in this relationally‐constituted cosmos? Finally, (...) how do these developments enrich our understandings of responsibility—to each other and to our private conceptions of God? (shrink)

Theology and science are both essential to the process of making sense of the world. Yet their relationship over the centuries has been largely adversarial. The Darwinian revolution, in particular, has necessitated a radical reinterpretation of the traditional dogma concerning creation. In this paper I discuss two general issues that presently obstruct communication between scientists and theologians in this arena and that are brought into acute focus by Wolfhart Pannenberg. First, the need to exercise care in the use of such (...) denotative concepts as field especially in understanding the Darwinian character of the evolutionary process is addressed. Second, the ontological room science necessarily leaves theology in this enterprise is considered. (shrink)

This paper views such distinctions as creation and degeneration or good and evil in the Eastern sense of unity in polarity rather than in the Western sense of dual, antagonistic principles. Hence it considers the thermodynamic forces of evolution as processes of creation driven by entropy dissipation and explores the analogies this conception bears to the Hindu image of nature as the changing mist of a universal breath. Using this image, the paper examines the sense in which the second law (...) of thermodynamics connects chance and teleology in the operations of nature and provides for a causal hierarchy in which decision and volitional behavior co‐participate with the laws of nature to determine the course of evolution. (shrink)

This disagreement extends to the fundamental details of physical and biochemical theories. On the other hand, (2) There is almostuniversal agreementthatlife did notfirstcome aboutmerely by chance. This is not to say that all scientists think that life’s existence was inevitable. The common view is that given a fuller understanding of the physical and biological conditions and processes involved, the emergence of life should be seen to be quite likely, or at least not very surprising. The view which is almost universally (...) rejected by researchers in the field is that the numerous and prima facie improbable physical and biological requirements for life all fell together just by a fluke, like so many dice tumbling out of a bag and landing all sixes. Most importantly, for the purposes of the following discussion, (3) The conviction that life did not arise largely by chance is treated as epistem- ically prior to the development of alternative theories. C 2007, Copyright the Authors Journal compilation C 2007, Blackwell Publishing, Inc. (shrink)

. Modern science is one form of knowledge, demarcated by its time (modernity) and by other “knowledges.” There is a fair amount of clarity as to what does not count as scientific, but there is a twilight zone of knowledges whose scientific status is ambivalent. In this zone the encounter between science and religion takes place. The particular contribution of religion and theology in this encounter is to call for an ethics of knowledge in the epistemological endeavors of science.

In this paper, we aim at identifying a concept of man that can represent a reference point for those who work or supervise social processes characterized by commercial or economic purposes. Economic, management, and organizational theories and ideas have a large impact on the way we think of ourselves, and we act accordingly. By making a radical departure from the ontological assumptions, this paper proposes a shifting of the current paradigm in terms of how we theorize about man. In order (...) to do this, we analyze the ontological level of the relationship between the idea of happiness and the concept of man from medieval scholastics, and the relationship between the idea of happiness and functionalism in social science. We first prove the formal equivalence between the structures of human choice as described in the qq. 6–21 Prima Secundae of the Summa Theologiae of St. Thomas Aquinas, and the model of problem-solving behavior as conceptualized in popular management models. Then we show that the Aquinas theory of action could provide a more adequate view of economy and business in the sociocultural and environmental context in which they operate. Finally, we present the implications of this study for management theory, practice, and education. (shrink)

Within cultural history there is a widespread eschewal of speculative reasoning. This article notes the complicity of the general postmodern avoidance of metanarratives with Anglo-Saxon empiricism and locates the major problem facing cultural history in postmodernism's conflation of trajectories and teleologies. Any discussion of the directionality of history is imputed to be a full-blown teleology. Using previous discussions from different fields, the difference between a teleology and trajectory is defended and, after clarifying certain confusions, it is argued that trajectories, as (...) following the working of generative mechanisms, are necessary to theorize in order to make interesting progress within the field of cultural history. (shrink)

Opatrzność Boża a przypadek w świecie Celem artykułu jest obrona dwóch tez: pierwszej, że istnienie zdarzeń przypadkowych jest do pogodzenia z istnieniem Boga oraz tezy drugiej, że przypadek może być częścią Bożej opatrzności. Koniunkcja obu powyższych tez nazwana jest w artykule tezą kompatybilizmu. Argumentacja w obronie kompatybilizmu opiera się na danych współczesnej nauki oraz na idei wszechmocnego Boga Stwórcy. Porządek argumentacji w artykule jest następujący. W części drugiej przedstawiony jest historyczny kontekst oraz podstawy doktrynalne pojęcia opatrzności. W części trzeciej omówiony (...) jest argument za nieistnieniem Boga oparty na założeniu głoszącym istnienie zdarzeń przypadkowych w świecie oraz przedstawiona jest krytyka tego argumentu. W części czwartej prezentowane są możliwe modele działania Boga w świecie, w ramach których przyjmuje się istnienie zdarzeń przypadkowych. W części piątej i ostatniej rozważana jest idea Bożej doskonałości obejmującej takie atrybuty jak wszechmoc, wszechwiedzę, doskonałą dobroć i suwerenną wolę Bożą. (shrink)

When Darwin's theory of natural selection threatened to put Paley's Designer out of a job, one response was to reemploy God as the author of the evolutionary process itself. This idea requires an account of how God might be understood to act in biological history. I approach this question in two stages: first, by considering God's action as creator of the world as a whole, and second, by exploring the idea of particular divine action in the course of evolution. As (...) creator ex nihilo God acts directly in every event as its sustaining ground. Because God structures the world as a lawful order of natural causes, God also acts indirectly by means of creatures. More controversially, God might act directly within the world to affect the course of events; this action need not take the form of a miraculous intervention, if the natural order includes the right sort of indeterministic chance. In each of these ways God's purposes can shape evolutionary processes. (shrink)

In "The Indeterministic Character of Evolutionary Theory: No 'Hidden Variables Proof' But No Room for Determinism Either," Brandon and Carson (1996) argue that evolutionary theory is statistical because the processes it describes are fundamentally statistical. In "Is Indeterminism the Source of the Statistical Character of Evolutionary Theory?" Graves, Horan, and Rosenberg (1999) argue in reply that the processes of evolutionary biology are fundamentally deterministic and that the statistical character of evolutionary theory is explained by epistemological rather than ontological considerations. In (...) this paper I focus on the topic of mutation. By focusing on some of the theory and research on this topic from early to late, I show how quantum indeterminism hooks up to point mutations (via tautomeric shifts, proton tunneling, and aqueous thermal motion). I conclude with a few thoughts on some of the wider implications of this topic. (shrink)

. Prospects for uniting religion and science are brightened by recently changed views of consciousness and mind‐brain interaction. Mental, vital, and spiritual forces, long excluded and denounced by materialist philosophy, are reinstated in nonmystical form. A revised scientific cosmology emerges in which reductive materialist interpretations emphasizing causal control from below upward are replaced by revised concepts that emphasize the reciprocal control exerted by higher emergent forces from above downward. Scientific views of ourselves and the world and the kinds of values (...) upheld by scientific belief undergo basic transformations, making them more compatible with religious motivation and moral responsibility. (shrink)

. The question of whether or not our universe is deterministic remains of interest to both scientists and theologians. In this essay I argue that this question can be solved only by metaphysical decision and that no scientific evidence for either determinism or indeterminism will ever be conclusive. No finite being, no matter how powerful its cognitive abilities, will ever be able to establish the deterministic nature of the universe. The only being that would be capable of doing so would (...) be one that is at once transcendent and immanent. Such a being is compatible with the God of the Christian tradition, which yields that a deterministic worldview is compatible with a deterministic worldview. A more important point is that because science is never able to establish the determinism of our universe, it can never definitely rule out divine action except on metaphysical grounds. (shrink)