The foundations of biology have been a topic of debate for the past few decades. The traditional perspective of the Modern Synthesis, which portrays organisms as passive entities with limited role in evolutionary theory, is giving way to a new paradigm where organisms are recognized as active agents, actively shaping their own phenotypic traits for adaptive purposes. Within this context, this article raises the question of whether contemporary biological theory is undergoing a cognitive revolution. This inquiry can be approached in (...) two ways: from a theoretical standpoint, exploring the centrality of the cognitive sciences in current theoretical biology; and from a historical perspective, examining the resemblance between the current state of theoretical biology and the Cognitive Revolution of the mid-20th century. Both inquiries yield affirmative answers, though important nuances will be emphasized. The cognitive sciences' explanatory framework is employed to elucidate the agentic characteristics of organisms, establishing a clear parallelism between the Cognitive Revolution and the present state of theoretical biology. (shrink)

Biological agency has received much attention in recent philosophy of biology. But what is the motivation for introducing talk of agency into biology and what is meant by “agent”? Two distinct motivations can be discerned. The first is that thinking of organisms as agents helps to articulate what is distinctive about organisms vis-à-vis other biological entities. The second is that treating organisms as agent-like is a useful heuristic for understanding their evolved behavior. The concept of agent itself may be understood (...) in at least four different ways: minimal agent, intelligent agent, rational agent, and intentional agent. Which understanding is most appropriate depends on which of the two motivations we are concerned with. (shrink)

Complex, multigenic biological traits are shaped by the emergent interaction of proteins being the main functional units at the molecular scale. Based on a phenomenological approach, algorithms for quantifying two different aspects of emergence were introduced (Wegner and Hao in Progr Biophys Mol Biol 161:54–61, 2021) describing: (i) pairwise reciprocal interactions of proteins mutually modifying their contribution to a complex trait (denoted as weak emergence), and (ii) formation of a new, complex trait by a set of n ‘constitutive’ proteins at (...) concentrations exceeding individual threshold values (strong emergence). The latter algorithm is modified here to take account of protein redundancy with respect to a complex trait (‘full redundancy’). Irreducibility is considered a necessary and sufficient criterion for strong biological emergence; if one constitutive protein is missing, or its concentration drops below the threshold the trait is lost. A definition based on ‘unpredictability’ is dismissed, because this criterion is irrelevant for the evolution of a complex trait, and apparent unpredictability may rather reflect our basic deficits in understanding unless we can provide an unequivocal proof for it. The phenomenological approach advocated here allows to identify hidden rules according to which strongly emergent traits may be organized. This is of high value for understanding the evolution of complex traits which seems to require the saltational advent of all constitutive proteins ‘in one turn’ to arrive at a functional trait providing for an improved fitness of the organism. Rather than being a purely random process, it may be guided by fundamental structural principles. (shrink)

We offer a general definition of interpretation based on a naturalized teleology. The definition tests and extends the biosemiotic paradigm by seeking to provide a philosophically robust resource for investigating the possible role of semiosis (processes of representation and interpretation) in biological systems. We show that our definition provides a way of understanding various possible kinds of misinterpretation, illustrate the definition using examples at the cellular and subcellular level, and test the definition by applying it to a potential counterexample. We (...) explain how we propose to use the definition as a way of asking new questions about what distinguishes life from non-life and of formulating testable hypotheses within the field of origin-of-life research. If the definition leads to fruitful new empirical approaches to the scientific problem of the origin of life, it will help to establish biosemiotics as a legitimate philosophical approach in theoretical biology and will thereby support a theological appropriation of the biosemiotic perspective as the basis of a new theology of nature. (shrink)

Recent work by Renaud Barbaras on the definition of life has shown the fecundity of a phenomenological approach that sees absence as having a positive status. This phenomenon allows Barbaras to identify life with “desire,” the indefinite exploration of the exterior world. It also allows Barbaras to defeat competing definitions of life in the sciences, particularly biology. In this paper, I propose a mutual complementarity between the work of Barbaras and that in contemporary systems science, namely by Stuart Kauffman, suggesting (...) that scientific concepts of subcriticality may allow for more overlap between phenomenological and scientific definitions of life than Barbaras acknowledges. (shrink)

We draw on Short’s work on Peirce’s theory of signs to propose a new general definition of interpretation. Short argues that Peirce’s semiotics rests on his naturalised teleology. Our proposal extends Short’s work by modifying his definition of interpretation so as to make it more generally applicable to putatively interpretative processes in biological systems. We use our definition as the basis of an account of different kinds of misinterpretation and we discuss some questions raised by the definition by reference to (...) parallel problems in the field of teleosemantics. We propose that interpretative responses fulfilling the criteria of our definition may be made by relatively simple molecular entities and we suggest two specific empirical applications of the definition to experimental work in the field of origin of life research. Our wider aim is to suggest that a well formulated naturalistic definition of interpretation will allow a re-evaluation of the role of semiotic phenomena in biological systems, including the generation of empirically testable hypotheses. (shrink)

This Afterword looks back over both parts of the discussion of “God and the World of Signs”—“Semiotics and the Emergence of Life” in the previous issue of Zygon and “Semiotics and Theology” in this issue. Three central questions in this extended debate are identified: What is the nature of biological organisms and biological evolution? What is the relationship between the natural world and the Triune God of the Christian theological tradition? What should be the goals of Science/Religion Studies? I summarize (...) the answers that Christopher Southgate and Andrew Robinson have given in their program and the challenges raised by their critics. Their strengths and weaknesses are assessed. In the conclusion I ask readers to imagine that this particular research program were to be taken as a model program in science-and-religion research (with some tweaking) and then consider the features of the program that could function as standards for scholars working in other areas of the dialogue. (shrink)

Scientific theories of consciousness identify its contents with the spatiotemporal structure of neural population activity. We follow up on this approach by stating and motivating Dynamical Emergence Theory, which defines the amount and structure of experience in terms of the intrinsic topology and geometry of a physical system’s collective dynamics. Specifically, we posit that distinct perceptual states correspond to coarse-grained macrostates reflecting an optimal partitioning of the system’s state space—a notion that aligns with several ideas and results from computational neuroscience (...) and cognitive psychology. We relate DET to existing work, offer predictions for empirical studies, and outline future research directions. (shrink)

Harold Saxton Burr was a biologist working throughout the 1930s–1950s on an important set of problems related to biological organization and the origin of complex living forms. He was a profound thinker, suggesting a complementary focus on field concepts in addition to the emphasis on particle models and integrating concepts from physics and philosophy in his work. He developed innovations in electrophysiological technique and used them to perform a wide experimental survey of bioelectricity in normal and pathological growth. Here, I (...) briefly review his classic paper with philosopher F. S. C. Northrop, “The Electro-Dynamic Theory of Life,” in the context of advances in this field over the last few decades. Based on recent progress, it is now clear that Burr was a prescient and visionary thinker. His main hypothesis, that bioelectric gradients serve as prepatterns guiding morphogenesis, has been confirmed using modern molecular physiology, as have his ideas about the place of cancer and the nervous system in the question of biological organization. With limited technology but deep insight, he derived insights that anticipated many modern discoveries. Even more importantly, Burr’s view of bioelectricity as a convenient entry point for rigorous investigation of the broader question of self-organizing properties of life highlights a frontier of inquiry that awaits today’s researchers. Burr and Northrop’s “The Electro-Dynamic Theory of Life,” originally published in the Quarterly Review of Biology :322–333, 1935), is available as supplementary material in the online version of this essay. (shrink)

In this article, I call into question the relevance of emergence theories as presently used by thinkers in the science–religion discussion. Specifically, I discuss theories of emergence that have been used by both religious naturalists and proponents of panentheism. I argue for the following conclusions: (1) If we take the background theory to be metaphysical realism, then there seems to be no positive connection between the reality of emergent properties and the validity of providing reality with a religious interpretation, though (...) one could perhaps construe an argument for the positive ontological status of emergence as a negative case for a religious worldview. (2) To be considered more plausible, religious naturalism should interpret religious discourse from the perspective of pragmatic realism. (3) Panentheistic models of divine causality are unable to avoid ontological dualism. (4) It is not obvious that emergent phenomena and/or properties are nonreducible in the ontological sense of the terms; indeed, the tension between weak and strong emergence makes it difficult for the emergentist to make ontological judgments. My general conclusion is that the concept of emergence has little metaphysical significance in the dialogue between science and theology. (shrink)

This paper provides a survey of contemporary religious naturalism. It presents reductive and non‐reductive versions of religious naturalism, and some arguments in favour of this naturalistic perspective. Finally, it discusses three crucial demarcation issues that contemporary religious naturalism faces.

In this article, I offer a critical evaluation of non-reductive physicalism as articulated and defended by Nancey Murphy. I argue that the examples given by Murphy do not illustrate robust emergence and the philosophical idea of downward causation. The thesis of multiple realizability is ontologically neutral, and so cannot support the idea of the causal efficacy of higher-level properties. Supervenience is incompatible with strong emergence. I also argue for the fruitful relationship between emergence theory and panpsychism pertaining to the metaphysical (...) issue of the origin and nature of mind. (shrink)

Big historians are attempting to construct a general holistic narrative of human origins enabling an approach to studying the emergence of complexity, the relation between evolutionary processes, and the modern context of human experience and actions. In this paper I attempt to explore the past and future of cosmic evolution within a big historical foundation characterized by physical, biological, and cultural eras of change. From this analysis I offer a model of the human future that includes an addition and/or reinterpretation (...) of technological singularity theory with a new theory of biocultural evolution focused on the potential birth of technological life: the theory of atechnogenesis. Furthermore, I explore the potential deep futures of technological life and extrapolate towards two hypothetical versions of an ‘Omega Civilization’: expansion and compression. (shrink)

Our aim in this article is to attempt to discuss propagating organization of process, a poorly articulated union of matter, energy, work, constraints and that vexed concept, “information”, which unite in far from equilibrium living physical systems. Our hope is to stimulate discussions by philosophers of biology and biologists to further clarify the concepts we discuss here. We place our discussion in the broad context of a “general biology”, properties that might well be found in life anywhere in the cosmos, (...) freed from the specific examples of terrestrial life after 3.8 billion years of evolution. By placing the discussion in this wider, if still hypothetical, context, we also try to place in context some of the extant discussion of information as intimately related to DNA, RNA and protein transcription and translation processes. While characteristic of current terrestrial life, there are no compelling grounds to suppose the same mechanisms would be involved in any life form able to evolve by heritable variation and natural selection. In turn, this allows us to discuss at least briefly, the focus of much of the philosophy of biology on population genetics, which, of course, assumes DNA, RNA, proteins, and other features of terrestrial life. Presumably, evolution by natural selection—and perhaps self-organization—could occur on many worlds via different causal mechanisms. Here we seek a non-reductionist explanation for the synthesis, accumulation, and propagation of information, work, and constraint, which we hope will provide some insight into both the biotic and abiotic universe, in terms of both molecular self reproduction and the basic work energy cycle where work is the constrained release of energy into a few degrees of freedom. The typical requirement for work itself is to construct those very constraints on the release of energy that then constitute further work. Information creation, we argue, arises in two ways: first information as natural selection assembling the very constraints on the release of energy that then constitutes work and the propagation of organization. Second, information in a more extended sense is “semiotic”, that is about the world or internal state of the organism and requires appropriate response. The idea is to combine ideas from biology, physics, and computer science, to formulate explanatory hypotheses on how information can be captured and rendered in the expected physical manifestation, which can then participate in the propagation of the organization of process in the expected biological work cycles to create the diversity in our observable biosphere. Our conclusions, to date, of this enquiry suggest a foundation which views information as the construction of constraints, which, in their physical manifestation, partially underlie the processes of evolution to dynamically determine the fitness of organisms within the context of a biotic universe. (shrink)

For the ancient Greeks, the world was both Eros, the god of chaos and creativity, and Logos, the regularity of the heavens as law. From chaos the world came forth. The world was home to ultimate creativity. Two thousand years later Kepler, Galileo, and then mighty Newton created deterministic classical physics in which all that happens in the universe is determined by the laws of motion, initial and boundary conditions. The Theistic God who worked miracles became the Deistic God who (...) set up the universe and let Newton’s laws take over. Eros, raw creativity, is dead, all is Logos.Quantum mechanics replaced the determinism of classical physics with fundamental indeterminism. This was a major crisis in physics, but remained entirely within the Newtonian paradigm of laws, here the Schrödinger equation, initial and boundary conditions. The Schrödinger equation entails the deterministic propagation of a probability distribution. The probabilities concern the indeterminate outcomes of quantum measurement events.The central issue of this article is to show that no laws at all determine or entail the becoming of our biosphere or any other among the 1022 solar systems in the universe. This claim is radical. If no laws determine or entail the becoming of biospheres, and biospheres are part of the universe, the Pythagorean dream that All is Number, All is Logos, is dead. There is no Final Theory that entails all that become in the universe. Eros is again, and always was, rambunctiously alive in the raw creativity of the becoming of life anywhere in the universe. The becoming of life is based on physics, on Logos, but beyond it, emerging from Eros.The reasons Eros is at play in the evolution of biospheres are fourfold.First, the universe will not make all possible complex things. That is, the universe is vastly non-ergodic. Yet complex things such as the human heart exist.Second, the reason human hearts exist is that organisms are Kantian Wholes in which the parts exist for and by means of the whole. Hearts exist because they fulfill the function of pumping the blood that keeps the whole organism alive. Such organisms propagate progeny that carry with them the hearts that keep them alive.Third, adaptations like hearts, the flagellar motor, the loop of Henle in kidneys that concentrates urine, and flight feathers, are tinkered-together contraptions stumbled upon in evolution. Parts and processes that arise in evolution are jury-rigged for unprestatable new functions that help keep the entire Kantian Whole organism alive and propagating in the evolving biosphere. There is no deductive theory of jury rigging. We cannot deduce the emergence of such novel functions.Fourth, the functions of parts of organisms emerge in unprestatable ways and form the unprestatable and ever-changing phase space of evolution. Since we cannot prestate the ever-changing phase space of evolution, we can write no laws of motion in differential equation form, so cannot integrate the equations we do not have. Thus, no laws entail the becoming of any biosphere.Evolving biospheres are everywhere creative. This is Eros, the chaos from which the world emerges. This profound creative emergence is the stuff of story, of narrative. Evolving biospheres always were and always will be both Eros and Logos, the stuff of story and the stuff of law. We always live in a world of Art and Science. (shrink)

Based on the conception of life and semiosis as co-extensive an attempt is given to classify cognitive and communicative potentials of species according to the plasticity and articulatory sophistication they exhibit. A clear distinction is drawn between semiosis and perception, where perception is seen as a high-level activity, an integrated product of a multitude of semiotic interactions inside or between bodies. Previous attempts at finding progressive trends in evolution that might justify a scaling of species from primitive to advanced levels (...) have not met with much success, but when evolution is considered in the light of semiosis such a scaling immediately catches the eye. The main purpose of this paper is to suggest a scaling of this progression in semiotic freedom into a series of distinct steps. The elleven steps suggested are: 1) molecular recognition, 2) prokaryote-eukaryote transformation, 3) division of labor in multicellular organisms, 4) from irritability to phenotypic plasticity, 5) sense perception, 6) behavioral choice, 7) active information gathering, 8) collaboration, deception, 9) learning and social intelligence, 10) sentience, 11) consciousness. In light of this, the paper finally discusses the conceptual framework for biosemiotic evolution. The evolution of biosemiotic capabilities does not take the form of an ongoing composition of simple signs into composite wholes. Rather, it takes the shape of the increasing subdivision and control of a primitive, holophrastic perception-action circuit already committed to “proto-propositions” reliably guiding action already in the most primitive species. (shrink)

A sign is something that refers to something else. Signs, whether of natural or cultural origin, act by provoking a receptive system, human or nonhuman, to form an interpretant (a movement or a brain activity) that somehow relates the system to this "something else." Semiotics sees meaning as connected to the formation of interpretants. In a biosemiotic understanding living systems are basically engaged in semiotic interactions, that is, interpretative processes, and organic evolution exhibits an inherent tendency toward an increase in (...) semiotic freedom. Mammals generally are equipped with more semiotic freedom than are their reptilian ancestor species, and fishes are more semiotically sophisticated than are invertebrates. The evolutionary trend toward the production of life forms with an increasing interpretative capacity or semiotic freedom implies that the production of meaning has become an essential survival parameter in later stages of evolution. (shrink)

The majority of G protein-coupled receptors (GPCRs) self-assemble in the form dimeric/oligomeric complexes along the plasma membrane. Due to the molecular interactions they participate, GPCRs can potentially provide the framework for discriminating a wide variety of intercellular signals, as based on some kind of combinatorial receptor codes. GPCRs can in fact transduce signals from the external milieu by modifying the activity of such intracellular proteins as adenylyl cyclases, phospholipases and ion channels via interactions with specific G-proteins. However, in spite of (...) the number of cell functions they can actually control, both GPCRs and their associated signal transduction pathways are extremely well conserved, for only a few alleles with null or minor functional alterations have so far been found. This would seem to suggest that, beside a mechanism for DNA repairing, there must be another level of quality control that may help maintaining GPCRs rather stable throughout evolution. We propose here receptor oligomerization to be a basic molecular mechanism controlling GPCRs redundancy in many different cell types, and the plasma membrane as the first hierarchical cell structure at which selective categorical sensing may occur. Categorical sensing can be seen as the cellular capacity for identifying and ordering complex patterns of mixed signals out of a contextual matrix, i.e., the recognition of meaningful patterns out of ubiquitous signals. In this context, redundancy and degeneracy may appear as the required feature to integrate the cell system into functional units of progressively higher hierarchical levels. (shrink)

Non-human animal chimeras, containing human neurological cells, have been created in the laboratory. Despite a great deal of debate, the status of such beings has not been resolved. Under normal definitions, such a being could either be unconventionally human or abnormally animal. Practical investigations in animal sentience, artificial intelligence, and now chimera research, suggest that such beings may be assumed to have no legal rights, so philosophy could provide a different answer. In this vein, therefore, we can ask: What would (...) a chimera, if it could think, think about? Thinking is used to capture the phenomena of a novel, chimeric being perceiving its terrible predicament as no more than a laboratory experiment. The creation of a thinking chimera therefore forces us to reconsider our assumptions about what makes human beings (potentially) unique (and other sentient animals different), because, as such, a chimera’s existence bridges our social and legal expectations about definitions of human and animal. Society has often evolved new social norms based on different kinds of (ir)rational contrivances; the imperative of non-contradiction, which is defended here, therefore requires a specific philosophical response to the rights of a thinking chimeric being. (shrink)

The publicity surrounding the recent McMath and Muñoz cases has rekindled public interest in brain death: the familiar term for human death determination by showing the irreversible cessation of clinical brain functions. The concept of brain death was developed decades ago to permit withdrawal of therapy in hopeless cases and to permit organ donation. It has become widely established medical practice, and laws permit it in all U.S. jurisdictions. Brain death has a biophilosophical justification as a standard for determining human (...) death but remains poorly understood by the public and by health professionals. The current controversies over brain death are largely restricted to the academy, but some practitioners express ambivalence over whether brain death is equivalent to human death. Brain death remains an accepted and sound concept, but more work is necessary to establish its biophilosophical justification and to educate health professionals and the public. (shrink)

Among the old and new controversies over brain death, none is more fundamental than whether brain death is equivalent to the biological phenomenon of human death. Here, I defend this equivalency by offering a brief conceptual justification for this view of brain death, a subject that Andrew Huang and I recently analyzed elsewhere in greater detail. My defense of the concept of brain death has evolved since Bernard Gert, Charles Culver, and I first addressed it in 1981, a development that (...) paralleled advances in intensive care unit treatment. The century‐old concept of the organism as a whole provides the fundamental justification for the equivalency of brain death and human death. In our technological age, in which increasing numbers of components and systems of an organism can be kept alive, and for longer intervals, the permanent cessation of functioning of the organism as a whole is the phenomenon that best corresponds to its death. (shrink)

In this review, we describe some of the central philosophical issues facing origins-of-life research and provide a targeted history of the developments that have led to the multidisciplinary field of origins-of-life studies. We outline these issues and developments to guide researchers and students from all fields. With respect to philosophy, we provide brief summaries of debates with respect to (1) definitions (or theories) of life, what life is and how research should be conducted in the absence of an accepted theory (...) of life, (2) the distinctions between synthetic, historical, and universal projects in origins-of-life studies, issues with strategies for inferring the origins of life, such as (3) the nature of the first living entities (the “bottom up” approach) and (4) how to infer the nature of the last universal common ancestor (the “top down” approach), and (5) the status of origins of life as a science. Each of these debates influences the others. Although there are clusters of researchers that agree on some answers to these issues, each of these debates is still open. With respect to history, we outline several independent paths that have led to some of the approaches now prevalent in origins-of-life studies. These include one path from early views of life through the scientific revolutions brought about by Linnaeus (von Linn.), Wöhler, Miller, and others. In this approach, new theories, tools, and evidence guide new thoughts about the nature of life and its origin.We also describe another family of paths motivated by a” circularity” approach to life, which is guided by such thinkers as Maturana & Varela, Gánti, Rosen, and others. These views echo ideas developed by Kant and Aristotle, though they do so using modern science in ways that produce exciting avenues of investigation. By exploring the history of these ideas, we can see how many of the issues that currently interest us have been guided by the contexts in which the ideas were developed. The disciplinary backgrounds of each of these scholars has influenced the questions they sought to answer, the experiments they envisioned, and the kinds of data they collected. We conclude by encouraging scientists and scholars in the humanities and social sciences to explore ways in which they can interact to provide a deeper understanding of the conceptual assumptions, structure, and history of origins-of-life research. This may be useful to help frame future research agendas and bring awareness to the multifaceted issues facing this challenging scientific question. (shrink)

Biosemiotics deal with the study of signs and meanings in living entities. Constructivism considers human knowledge as internally constructed by sense making rather than passively reflecting a pre-existing reality. Consequently, a constructivist perspective on biosemiotics leads to look at an internal active construction of meaning in living entities from basic life to humans. That subject is addressed with an existing tool: the Meaning Generator System (MGS) which is a system submitted to an internal constraint related to the nature of the (...) agent containing it (biological or artificial). Simple organisms generate meanings to satisfy a “stay alive” constraint. More complex living entities manage meaningful representations with more elaborated constraints. The generated meanings are used by the agents to implement actions aimed at satisfying the constraints. The actions can be physical, biological or mental and take place in the agent or in its environment. The case of human agency is introduced with meaningful representations that may have allowed our ancestors to become self-conscious by representing themselves as existing entities. This paper proposes to use the MGS as a thread to address the above items linking biosemiotics to constructivism with relations to normativity, agency and autonomy. Possible continuations are introduced. (shrink)