Complexity in Biology

Advances in biology, at least over the past two centuries, have mostly relied on theories that were subsequently revised, expanded or eventually refuted using experimental and other means. The field of theoretical biology used to primarily provide a basis, similar to theoretical physics in the physical sciences, to rationally examine the frameworks within which biological experiments were carried out and to shed light on overlooked gaps in understanding. Today, however, theoretical biology has generally become synonymous with computational and mathematical biology. (...) This could in part be explained by a relatively recent tendency in which a "data first", rather than a "theory first", approach is preferred. Moreover, generating hypotheses has at times become procedural rather than theoretical, therefore perhaps inadvertently leading some hypotheses to become perfunctory in nature. This situation leaves our understanding enmeshed in data, which should be disentangled from much noise. Given the many unresolved questions in biology and medicine, big and small, ranging from the problem of protein folding to unifying causative frameworks of complex non-Mendelian human diseases, it seems apt to revive the role of pure theory in the biological sciences. This paper, using the current biomedical literature and historical precedents, makes the case for a "philosophical biology" (philbiology), distinct from but quite complementary to philosophy of biology (philobiology), which would entail biological investigation through philosophical approaches. Philbiology would thus be a reincarnation of theoretical biology, adopting the true sense of the word "theory" and making use of a rich tradition of serious philosophical approaches in the natural sciences. A philbiological investigation, after clearly defining a given biological problem, would aim to propose a set of empirical questions, along with a class of possible solutions, about that problem. Importantly, whether or not the questions can be tested using current experimental paradigms would be secondary to whether the questions are inherently empirical or not. These issues will be illustrated using a range of specific examples. The final goal of a philbiological investigation would be to develop a theoretical framework that can lead observational and/or interventional experimental studies of the defined problem, a framework that is structured, generative and expandable, and, crucially, one that simplifies some aspect(s) of the said problem. (shrink)

Bedau's influential (1997) account analyzes weak emergence in terms of the non-derivability of a system’s macrostates from its microstates except by simulation. I offer an improved version of Bedau’s account of weak emergence in light of insights from information theory. Non-derivability alone does not guarantee that a system’s macrostates are weakly emergent. Rather, it is non-derivability plus the algorithmic compressibility of the system’s macrostates that makes them weakly emergent. I argue that the resulting information-theoretic picture provides a metaphysical account of (...) weak emergence rather than a merely epistemic one. (shrink)

This paper investigates the degree to which information theory, and the derived uses that make it work as a metaphor of our age, can be helpful in thinking about God’s immanence and transcendance. We ask when it is possible to say that a consciousness has to be behind the information we encounter. If God is to be thought about as a communicator of information, we need to ask whether a communication system has to pre-exist to the divine and impose itself (...) to God. If we want God to be Creator, and not someone who would work like a human being, ‘creating’ will mean sustaining in being as much the channel, the material system, as the message. Is information control? It seems that God’s actions are not going to be informational control of everything. To clarify the issue, we attempt to distinguish two kinds of ‘genialities’ in nature, as a way to evaluate the likelihood of God from nature. We investigate concepts and images of God, in terms of the history of ideas but also in terms of philosophical theology, metaphysics, and religious ontology. (shrink)

The task of this essay is to put biological individuals in formal terms. This approach is not directly interested in matters of time (for example, in evolution), but rather in the formal shape of biological objects. So it is different from, but not opposed to, natural science. In his later years, Wittgenstein made similar investigations in psychology and mathematics. Unfortunately, he found no time to make extensive remarks on philosophy of biology. This is what we are going to advance here.

In 1926, Haldane published an essay titled 'On Being the Right Size' in which he argued that the structure, function, and behavior of an organism are strongly conditioned by the physical forces that exert the greatest impact at the scale at which it exists. This chapter puts Haldane’s insight to work in the context of contemporary cell and molecular biology. Owing to their minuscule size, cells and molecules are subject to very different forces than macroscopic organisms. In a sense, macroscopic (...) and microscopic entities inhabit different “worlds”: the former is ruled by gravity and inertia, whereas the latter is governed by Brownian motion. One implication is that we should be extremely skeptical of models and analogies that seek to explain properties of microscopic entities by appealing to properties of macroscopic ones. Unfortunately, this is precisely what the appeal to engineering metaphors in molecular biology attempts to do. Molecular biologists routinely resort to such metaphors because they are familiar and intuitively intelligible. But if our machines were the size of molecules it would be impossible for them to function the way they do. It follows that we should avoid distorting biological reality by construing it in engineering terms. In this chapter I examine four key metaphors in molecular biology – “genetic program,” “cellular circuitry,” “molecular machine,” and “molecular motor” – and I argue that their deficiencies derive from their neglect of scale. I also try to explain why many biologists today appear to have forgotten the importance of scale that Haldane drew attention to in his essay. I suggest that the reason has to do with the influence of Schrödinger’s argument in 'What is Life?' regarding the stability of the gene. (shrink)

Has science already answered the fundamental questions about the concepts of Life, Cosmos and Evolution? Has science not relegated these fundamental questions by following up on more immediate, “useful” and practical endeavors that ultimately ensure that the wheel of capitalism keeps spinning in its frantic search for material and economic progress? There is something terribly wrong with the current theory of evolution, understood as the Darwinian theory with its successive versions and extensions. The concept of natural selection, the cornerstone of (...) Darwinism, is logically inconsistent. This has been demonstrated in some of my latest academic publications. The entire conceptual framework of Darwinism is inadequate. Organisms do not compete with each other for the survival of the fittest. The fundamental relationship in Nature is not competition or confrontation, but interconnectivity, complementarity, and relational meaningfulness. A new theory of evolution is necessary to explain how it is possible that organisms as simple as bacteria, protozoa and diatoms could have generated organisms as complex as primates, and among them, the human being, a being capable of feeling and thinking, of suffering and enjoying, a being capable of having ideals and purposes. A theory that explains how it is possible that this being so complex, rich, and to some extent still unknown, has emerged from a single cell, an egg-cell, lacking all the capacities, riches and depths of human existence. Such a theory already exists. (shrink)

This paper challenges the common assumption that some phenotypic traits are quantitative while others are qualitative. The distinction between these two kinds of traits is widely influential in biological and biomedical research as well as in scientific education and communication. This is probably due to both historical and epistemological reasons. However, the quantitative/qualitative distinction involves a variety of simplifications on the genetic causes of phenotypic variability and on the development of complex traits. Here, I examine three cases from the life (...) sciences that show inconsistencies in the distinction: Mendelian traits, Mendelian diseases, and polygenic mental disorders. I show that these traits can be framed both quantitatively and qualitatively depending, for instance, on the methods through which they are investigated and on specific epistemic purposes. This suggests that the received view of quantitative and qualitative traits has a limited heuristic power—limited to some local contexts or to the specific methodologies adopted. Throughout the paper, I provide directions for framing phenotypes beyond the quantitative/qualitative distinction. I conclude by pointing at the necessity of developing a principled characterisation of what phenotypic traits, in general, are. (shrink)

The central question in the biological sciences for the past 100 years has concerned an understanding of how living systems differ from other general physical phenomena and what makes these systems unique. With new developments in the fields of nonequilibrium thermodynamics, systems theory, chaos, and information theory over the past few decades, there has been growing interest in finally answering the question first posed by Erwin Schrödinger in the 1940s concerning the true scientific nature of living systems. Similarly, there is (...) also increasing interest within the biologic community for a more holistic and non-reductionist methodology. The approach followed in this book builds on a foundation of information theory and semiotics while integrating basic thermodynamic considerations and systems theory to form a singular unifying concept that is proposed to be the essential process of living systems. However, the premise presented is much more than simply the exposition of a new hypothesis. This book describes the logical progression of thought incorporating a diverse array of established scientific ideas that were used in the conceptualization of a dynamic mathematical framework that can be employed as a novel analytic means for the study of living systems and their fundamental processes. (shrink)

Philosophy of immunology is a subfield of philosophy of biology dealing with ontological and epistemological issues related to the studies of the immune system. While speculative investigations and abstract analyses have always been part of immune theorizing, until recently philosophers have largely ignored immunology. Yet the implications for understanding the philosophical basis of organismal functions framed by immunity offer new perspectives on fundamental questions of biology and medicine. Developed in the context of history of medicine, theoretical biology, and medical anthropology, (...) philosophy of immunology differs from these related branches of study in its focus on traditional philosophical questions concerning identity, individuality, ecology, cognition, scientific methodology and theory construction. This broad agenda derives from immunology’s multifaceted research program that has developed from its initial clinical challenges of host defense, transplantation, autoimmunity, tumor immunology, and allergy. In addition to these well-established research areas, immunity is now understood to play a central role in other physiological functions, development, ecology, and evolutionary mechanics. Holding together these diverse domains of inquiry lie philosophical commitments oriented by organismal identity. In this regard, pertinent issues are raised concerning cognition (organization of immune perception and information processing), the character of individuality (framed by the ecological context of immune-mediated assimilation and rejection), and the dynamics of complex systems (understood as holistic systems biology). Indeed, immunology, in the context of cognitive science, evolutionary biology, environmental sciences, and development provides multi-focal perspectives for philosophy of science. (shrink)

This note discusses the importance of Natural History (biology) in the development of Aristotle philosophy and scientific outlook, and so the importance of considering Aristotle's philosophy as a necessary and useful background for contemporary biology.

Among those speaking in the name of materialism, whether speculative, dialectical, or "new," it is commonplace to dismiss with a single gesture a vast field of theoretical and philosophical endeavor, indicated as the last 50 or 250 years of theory and philosophy. Self-styled "speculative" writers who would surpass all philosophy since Kant, and various New Materialists who sequester decades of thought under the heading of "constructivism," manufacture the avant-garde status of their own work by claiming to delineate a simple break (...) with the past. We would be at a loss, and perhaps at risk of missing the point, if we sought to uncover the common essence underlying this "new" work, either by looking for an agreement... (shrink)

Contemporary philosophy of science has seen a growing trend towards a focus on scientific practice over the epistemic outputs that such practices produce. This practice-oriented approach has yielded a clearer understanding of how reductive research strategies play a central role in contemporary scientific inquiry. In parallel, a growing body of work has sought to explore the role of non-reductive, or systems-level, research strategies. As a result, the relationship between reductive and non-reductive scientific practices is becoming of increased importance. In this (...) paper, I provide a framework within which research strategies can be compared. I argue that no strategy is reductive or non-reductive simpliciter, rather strategies are more, or are less, reductive than one another according to a frame of reference. That frame of reference is provided by a continuum of possible ways in which the target system might be conceptualised. I illustrate the utility of the framework by deploying it to analyse a recent debate in cancer research. When set within the framework, a prominent reductive strategy—the somatic mutation theory—and a prominent non-reductive strategy—the tissue organisational field theory—do not stand opposed to one another. Rather, they serve as boundary markers to chart the territory of approaches to carcinogenesis within which most strategies in the field fall. (shrink)

The aim of this paper is to provide a theoretical framework to understand how multicellular systems realize functionally integrated physiological entities by organizing their intercellular space. From a perspective centered on physiology and integration, biological systems are often characterized as organized in such a way that they realize metabolic self-production and self-maintenance. The existence and activity of their components rely on the network they realize and on the continuous management of the exchange of matter and energy with their environment. One (...) of the virtues of the organismic approach focused on organization is that it can provide an understanding of how biological systems are functionally integrated into coherent wholes. Organismic frameworks have been primarily developed by focusing on unicellular life. Multicellularity, however, presents additional challenges to our understanding of biological systems, related to how cells are capable to live together in higher-order entities, in such a way that some of their features and behaviors are constrained and controlled by the system they realize. Whereas most accounts of multicellularity focus on cell differentiation and increase in size as the main elements to understand biological systems at this level of organization, we argue that these factors are insufficient to provide an understanding of how cells are physically and functionally integrated in a coherent system. In this paper, we provide a new theoretical framework to understand multicellularity, capable to overcome these issues. Our thesis is that one of the fundamental theoretical principles to understand multicellularity, which is missing or underdeveloped in current accounts, is the functional organization of the intercellular space. In our view, the capability to be organized in space plays a central role in this context, as it enables (and allows to exploit all the implications of) cell differentiation and increase in size, and even specialized functions such as immunity. We argue that the extracellular matrix plays a crucial active role in this respect, as an evolutionary ancient and specific (non-cellular) control subsystem that contributes as a key actor to the functional specification of the multicellular space and to modulate cell fate and behavior. We also analyze how multicellular systems exert control upon internal movement and communication. Finally, we show how the organization of space is involved in some of the failures of multicellular organization, such as aging and cancer. (shrink)

Lynch, Parke, and O’Malley highlight the need for better evaluative criteria for causal explanations in microbiome research. They propose new interventionist criteria, show that paradigmatic examples of microbiome explanations are flawed using those criteria, and suggest numerous ways microbiome explanations can be improved. While we endorse their primary criticisms and suggestions for improvements in microbiome research, we make several observations regarding the use of mooted causal models in microbiome research that have significant implications for their overall argument. In sum, we (...) contend that their critique is too modest and that even flawed causal inferences like those they criticize can be valuable for generating better causal models and evaluating explanatory outcomes in individual cases. (shrink)

The fracture in the emerging discipline of biosemiotics when the code biologist Marcello Barbieri claimed that Peircian biosemiotics is not genuine science raises anew the question: What is science? When it comes to radically new approaches in science, there is no simple answer to this question, because if successful, these new approaches change what is understood to be science. This is what Galileo, Darwin and Einstein did to science, and with quantum theory, opposing interpretations are not merely about what theory (...) is right, but what is real science. Peirce's work, as he acknowledged, is really a continuation of efforts of Schelling to challenge the heritage of Newtonian science for the very good reason that the deep assumptions of Newtonian science had made sentient life, human consciousness and free will unintelligible, the condition for there being science. Pointing out the need for such a revolution in science has not succeeded as a defence of Peircian biosemiotics, however. In this paper, I will defend the scientific credentials of Peircian biosemiotics by relating it to the theoretical biology of the bio-mathematician, Robert Rosen. Rosen's relational biology, focusing on anticipatory systems and giving a place to final causes, should also be seen as a rigorous development of the Schellingian project to conceive nature in such a way that the emergence of sentient life, mind and science are intelligible. Rosen has made a very strong case for the characterization of his ideas as a real advance not only in science, but in how science should be understood, and I will argue that it is possible to provide a strong defence of Peircian biosemiotics as science through Rosen's defence of relational biology. In the process, I will show how biosemiotics can and should become a crucial component of anticipatory systems theory. (shrink)

The topic of the relationship between the organism and its environment runs through the theories of Uexküll, Goldstein and Canguilhem with equal importance. In this work a counterpoint will be established between their theories, in the attempt to assess at which points the melodies are concordant and at which points they are discordant. As fundamental basis to his theory, Uexküll relies on the concept of conformity to a plan, which allows him to account for the congruity and perfect adjustment between (...) organisms and their Umwelten. For Goldstein and Canguilhem, the relationship between an organism and its environment resembles instead a debate or coming to terms, in which the organism, as to ensure the continuity of the state of health, must constantly create norms to maintain a productive relationship with its environment. The pinpointing of these conceptual frameworks allows to lay emphasis on that each theory relies on specific assumptions regarding teleology and sense in organisms, as well as on specific definitions of the concept of life in general. Ultimately, the view that organisms and their environments have an original and common source, a principle, or plan, which must possess all the creative characteristics of life, will be seen as prevailing. (shrink)

In this work the doctrine of organicism will be addressed, as explained and seen mainly by Bertalanffy. We will study how this doctrine represents and embodies the ambiguity of Kantian teleology as a regulative principle, and how this same problem leads to consider a real problem as a knowledge problem. It will be concluded that organicism, conceived in this way, does not represent a true holism, but what we will call a syn-holism, a synthesis or assembly, and that to obtain (...) a true holism we must resort to the concept of true form. Finally, it will be established that since the fundamental characteristic of an organism is its development, a historical theory of the organism is required for which the concept of field can be useful and necessary. (shrink)

A notion of delegated causality is introduced here. This subtle kind of causality is dual to interventional causality. Delegated causality elucidates the causal role of dynamical systems at the “edge of chaos”, explicates evident cases of downward causation, and relates emergent phenomena to Gödel’s incompleteness theorem. Apparently rich implications are noticed in biology and Chinese philosophy. The perspective of delegated causality supports cognitive interpretations of self-organization and evolution.

In the last decade, Systems Biology has emerged as a conceptual and explanatory alternative to reductionist-based approaches in molecular biology. However, the foundations of this new discipline need to be fleshed out more carefully. In this paper, we claim that a relational ontology is a necessary tool to ground both the conceptual and explanatory aspects of Systems Biology. A relational ontology holds that relations are prior—both conceptually and explanatory—to entities, and that in the biological realm entities are defined primarily by (...) the context they are embedded within—and hence by the web of relations they are part of. (shrink)

The concept of 'levels of organization' has come under fire recently as being useless for scientific and philosophical purposes. In this paper, we show that 'levels' is actually a remarkably resilient and constructive conceptual tool that can be, and in fact is, used for a variety of purposes. To this effect, we articulate an account of the importance of the levels concept seen in light of its status as a major organizing concept of biology. We argue that the usefulness of (...) ‘levels’ is best seen in the heuristic contributions the concept makes to treating and structuring scientific problems. We illustrate this with two examples from biological research. (shrink)

Many have argued that there is no reason why natural selection should cause directional increases in measures such as body size or complexity across evolutionary history as a whole. In this paper I argue that this conclusion does not hold for selection for adaptations to environmental variability, and that, given the inevitability of environmental variability, trends in adaptations to variability are an expected feature of evolution by natural selection. As a concrete instance of this causal structure, I outline how this (...) may be applied to a trend in phenotypic plasticity. (shrink)

The ‘managed-metabolism’ hypothesis suggests that a ‘cooperation barrier’ must be overcome if self-producing chemical organizations are to undergo the transition from non-life to life. This dynamical barrier prevents un-managed autocatalytic networks of molecular species from individuating into complex, cooperative organizations. The barrier arises because molecular species that could otherwise make significant cooperative contributions to the success of an organization will often not be supported within the organization, and because side reactions and other ‘free-riding’ processes will undermine cooperation. As a result, (...) the barrier seriously impedes the emergence of individuality, complex functionality and the transition to life. This barrier is analogous to the cooperation barrier that also impedes the emergence of complex cooperation at all levels of living organization. As has been shown at other levels of organization, the barrier can be overcome comprehensively by appropriate ‘management’. Management implements a system of evolvable constraints that can overcome the cooperation barrier by ensuring that beneficial co-operators are supported within the organization and by suppressing free-riders. In this way, management can control and manipulate the chemical processes of a collectively autocatalytic organization, producing novel processes that serve the interests of the organization as a whole and that could not arise and persist in an un-managed chemical organization. Management self-organizes because it is able to capture some of the benefits that are produced when its interventions promote cooperation, thereby enhancing productivity. Selection will therefore favour the emergence of managers that take over and manage chemical organizations so as to overcome the cooperation barrier. The managed-metabolism hypothesis demonstrates that if management is to overcome the cooperation barrier comprehensively, its interventions must be digitally coded. In this way, the hypothesis accounts for the two-tiered structure of all living cells in which a digitally-coded genetic apparatus manages an analogically-informed metabolism.GraphicalOpen image in new window. (shrink)

The aim of the book is to explore common concerns regarding methodological individualism in different fields of the life sciences broadly construed. It will address conceptual problems regarding individuals and their relation and dependence on the collectivities they are part of and consider innovative new viewpoints, grounded in specific scientific projects that question the present descriptions and understanding and raise challenges. A wide variety of recent, influential contributions in the life sciences utilize notions of collectivity, sociality, rich interactions and emergent (...) phenomena, as essential explanatory tools to handle numerous persistent scientific questions in the life sciences. -/- Examples range from gene expression and regulation, the dynamics of bacterial populations, the ecological developmental biology of symbiosis, levels of selection, to communication, motion and patterns of behavior in diverse life forms, the role of social institutions and cultural dynamics in human evolution, and the psychological basis for social norms. The book is being structured so that fruitful and rewarding disciplinary interactions take place among researchers and scholars who have been concerned with overcoming methodological individualism. -/- The books includes a section of four papers on holobionts and the hologenome theory and a special memorial article on the work of the late Prof. Eshel Ben-Jacob authored by Herbert Levine. (shrink)

Why the replication crisis might be less severe than it seems at first.

Synthetic biology offers a powerful method to design and construct biological devices for human purposes. Two prominent design methodologies are currently used. Rational design adapts the design methodology of traditional engineering sciences, such as mechanical engineering. Directed evolution, in contrast, models its design principles after natural evolution, as it attempts to design and improve systems by guiding them to evolve in a certain direction. Previous work has argued that the primary difference between these two is the way they treat variation: (...) rational design attempts to suppress it, whilst direct evolution utilizes variation. I argue that this contrast is too simplistic, as it fails to distinguish different types of variation and different phases of design in synthetic biology. I outline three types of variation and show how they influence the construction of synthetic biological systems during the design process. Viewing the two design approaches with these more fine-grained distinctions provides a better understanding of the methodological differences and respective benefits of rational design and directed evolution, and clarifies the constraints and choices that the different design approaches must deal with. (shrink)

This is an epistemologically-driven history of the concept of evolution. Starting from its inception, this work will follow the development of this pregnant concept. However, in contradistinction to previous attempts, the objective will not be the identification of the different meanings it adopted through history, but conversely, it will let the concept to be unfolded, to be explicated and to express its own inner potentialities. The underlying thesis of the present work is, therefore, that the path that leads to the (...) development of the concept of evolution is the path that studies the possibilities of the evolution of concepts, and that the historical reconstruction of its conceptual trajectory will shed light into potential and unexploited possibilities. This methodology will provide useful tools and resources for future developments of the concept. For example, it will define the concept of transmutation as a different conceptual trajectory deviating from the one corresponding to evolution, at the onset of the 19th century. Moreover, epigenesis will not be the opposing concept to evolution, but only to simultaneous and instantaneous generation. It will demonstrate that every important system of epigenesis drew upon some kind of formative power to explain development. More importantly, it will show that the problem of preformation cannot be overlooked, and that some kind of virtual preformation must be considered in order to address the problems of generation and development. (shrink)

A long-standing debate on the causality of levels in biological explanations has divided philosophers into two camps. The reductionist camp insists on the causal primacy of lower, molecular levels, while the critics point out the inescapable shifting, reciprocity, and circularity of levels across biological explanations. We argue, however, that many explanations in biology do not exclusively draw their explanatory power from detailed insights into inter-level interactions; they predominantly require identifying the adequate levels of biological complexity to be explained. Moreover, the (...) main explanatory strategies grounding both theoretical and experimental approaches to one of the central debates in contemporary biology, i.e., on the origin of life, are primarily and sometimes exclusively driven by issues concerning the levels of biochemical complexity, and these only subsequently frame more substantial and detailed accounts of inter-level biochemical interactions. (shrink)

The problem of defining the self has traditionally been conceived as a task for philosophers. However, the development of immunology in the second part of the 20th century has led many scientists to conclude that immunology is the science of the self. This led to two different approaches to biological individuality: physiological individuation that is mostly concerned with organisms seen as strongly cohesive and unified metabolic entities, and evolutionary individuation where evolution by natural selection is seen as the best framework (...) for individuating biological entities. I discuss physiological approaches to biological individuation with a special focus on the immunological theories of the self. I argue that the immunological theories can only function as vague metaphors that do not provide a valid criterion for individuating organisms in biology. (shrink)

Contrary to concerns of some critics, we present evidence that biomedical research is not dominated by a small handful of model organisms. An exhaustive analysis of research literature suggests that the diversity of experimental organisms in biomedical research has increased substantially since 1975. There has been a longstanding worry that organism‐centric funding policies can lead to biases in experimental organism choice, and thus negatively impact the direction of research and the interpretation of results. Critics have argued that a focus on (...) model organisms has unduly constrained the diversity of experimental organisms. The availability of large electronic databases of scientific literature, combined with interest in quantitative methods among philosophers of science, presents new opportunities for data‐driven investigations into organism choice in biomedical research. The diversity of organisms used in NIH‐funded research may be considerably lower than in the broader biomedical sciences, and may be subject to greater constraints on organism choice. (shrink)

I look back at my 1996 book Complexity and the Function of Mind in Nature, responding to papers by Pamela Lyon, Fred Keijzer and Argyris Arnellos, and Matt Grove.

Phototoxicity frequently occurs during live fluorescence microscopy, and its consequences are often underestimated. Damage to cellular macromolecules upon excitation light illumination can impair sample physiology, and even lead to sample death. In this review, we explain how phototoxicity influences live samples, and we highlight that, besides the obvious effects of phototoxicity, there are often subtler consequences of illumination that are imperceptible when only the morphology of samples is examined. Such less apparent manifestations of phototoxicity are equally problematic, and can change (...) the conclusions drawn from an experiment. Thus, limiting phototoxicity is a prerequisite for obtaining reproducible quantitative data on biological processes. We present strategies to reduce phototoxicity, e.g. limiting the illumination to the focal plane and suggest controls for phototoxicity effects. Overall, we argue that phototoxicity needs increased attention from researchers when designing experiments, and when evaluating research findings. (shrink)

This edited collection showcases some of the best recent research in the philosophy of science. It comprises of thematically arranged papers presented at the 5th conference of the European Philosophy of Science Association (EPSA15), covering a broad variety of topics within general philosophy of science, and philosophical issues pertaining to specific sciences. The collection will appeal to researchers with an interest in the philosophical underpinnings of their own discipline, and to philosophers who wish to study the latest work on the (...) themes discussed. (shrink)

In this paper I analyze the process by which modelers in systems biology arrive at an adequate representation of the biological structures thought to underlie data gathered from high-throughput experiments. Contrary to views that causal claims and explanations are rare in systems biology, I argue that in many studies of gene regulatory networks modelers aim at a representation of causal structure. In addressing modeling challenges, they draw on assumptions informed by theory and pragmatic considerations in a manner that is guided (...) by an interventionist conception of causal structure. While doubts have been raised about the applicability of this notion of causality to complex biological systems, it is here seen to be an adequate guide to inquiry. (shrink)

A new approach to landscape ecology involves the application of the eco-field hypothesis and the General Theory of Resources. In this study, we describe the putative eco-field of bark beetles as a spatial configuration with a specific meaning-carrier for every organism-resource interaction. Bark beetles are insects with key roles in matter and energy cycles in coniferous forests, which cause significant changes to forestry landscapes when outbreaks occur. Bark beetles are guided towards host trees by the recognition of semiotic signals using (...) a specific eco-field. These signals mainly comprise a group of scents, which are called the odourtope. Their interactions with other organisms occur by sharing relevant information from the eco-field networks in the forest ecosystem. The eco-field networks modulate the expansion of the realized semiotic niche of the bark beetle towards the potential semiotic niche. Moreover, the niche construction process can be initiated by interchanging signals among species living in the same place, where these signals allow the exploitation of the required resources. If different organisms are interdependent on signals in eco-field networks, then this process may result in the establishment of mutualistic relationships. This is an example of how evolutionary processes are initiated by the recognition of signals in a network of eco-fields. (shrink)

We argue that constructive approaches in epistemology and systems science, which are focused on normativity, knowledge, and communication of organisms and emphasize the primacy of activity, self-construction, and niche-construction in the cognitive agents, fit naturally to the both methodology and theory of biosemiotics. In particular, constructive view was already present in the works of the major precursors of biosemiotics: von Uexküll and Bateson, and to some extent Peirce. Biosemiotics has a chance to function as a mediating field in the theoretical (...) integration of semiotics with its construction-related sister disciplines (e.g., second order cybernetics, autopoiesis, constructivism, enactivism, and interactivism) because of its explicit assumption of the semiotic nature of life and agency and its objectified “first person” view to biosemiotic agents, the view that nevertheless avoids the agnostic attitude towards reality. (shrink)

While Bayesian methods have become very popular in phylogenetic systematics, the foundations of this approach remain controversial. The star-tree paradox in Bayesian phylogenetics refers to the phenomenon that a particular binary phylogenetic tree sometimes has a very high posterior probability even though a star tree generates the data. I argue that this phenomenon reveals an unattractive feature of the Bayesian approach to scientific inference and discuss two proposals for how to address the star-tree paradox. In particular, I defend the polytomy (...) prior as a solution of the paradox and argue that it is preferable to a data-size dependent branch lengths prior from a methodological perspective. However, while this reply dissolves the star-tree paradox, the general challenge to Bayesian confirmation theory remains unmet. (shrink)

In business administration or in economics it is absolutely relevant not to consider indexes like profit growth rate or gross domestic product as exhaustive indexes for economic wealth. Likewise, in biology it is important not to confuse the representation of life with life itself. The most important concepts in biology are information, memory, structure, plasticity, and robustness. Information is the difference that makes the difference. Memories are information registered in an organism. Plasticity is the capacity of a living organism to (...) change its own structure/sets of behaviors for having a competitive advantage. Robustness is the ability of a living organism to resist environmental changes without changing its own structure/sets of behavior, and fragility is when a living organism undergoes changes in its own structure without being able to resist non-adaptive changes. (shrink)

Michael Ghiselin and David Hull’s individuality thesis is that biological species are individuals. Philosophers often treat the term “individual” as synonymous with “mereological sum” and characterize it in terms of mereology. It is easy to see how the biological project has been interpreted as a mereological one. This chapter argues that this is a mistake, that biological part/whole relations often violate the axioms of mereology. Conflating these projects confuses the central issues at stake in both, and makes the job of (...) evaluating either unnecessarily burdensome. Clarifying this helps identify the genuine metaphysical implications of the individuality thesis, which serves as an exemplar of scientifically informed metaphysics. (shrink)

This article interprets Jakob von Uexkull’s understanding of different beings’ Innenwelt, Gegenwelt, and umwelt through Deleuzian insights of multiplicity, context, and particularity. This Deleuzian interpolation into Uexkull’s insights acknowledges the absence of a unitary ‘human’ view of nature, recognizing instead that plural viewpoints of cultures, subgroups and individuals understand and interpret natural signs variously not just because of ideology but because of physiology and contrastive fundamental ways of accessing the world. Recent formative research in comparative neurobiology suggests that universal anthropological (...) claims of cross-cultural semiotic similarity are incorrect.Interpreting biosemiotics as the investigation of apprehending the Innenwelt of radically different others, such semiotic understandings themselves are not necessarily generalizable between different members of the same species in a group, same-species groups in different natural cultural contexts, or even the same animal at different points of time. Conjoining Deleuze’s insights of the complexity of multiplicity with Uexkull’s scientific-imaginative system of comprehending other creatures’ ways of understanding their world offers an increased self-reflexivity regarding the simultaneous levels of actual semiotic activity for biosemiotic inquiry. (shrink)

This paper examines the adequacy of causal graph theory as a tool for modeling biological phenomena and formalizing biological explanations. I point out that the causal graph approach reaches it limits when it comes to modeling biological phenomena that involve complex spatial and structural relations. Using a case study from molecular biology, DNA-binding and -recognition of proteins, I argue that causal graph models fail to adequately represent and explain causal phenomena in this field. The inadequacy of these models is due (...) to their failure to include relevant spatial and structural information in a way that does not render the model non-explanatory, unmanageable, or inconsistent with basic assumptions of causal graph theory. (shrink)

The intellectual act of imposing borders to contain and delimit objects has been a constituent factor in physics since its origins, and is also fundamental for philosophical reflection. However, the characteristics of the conceptual universe thus constructed (tendency towards the ideal limit, invariance in variation, a conception of matter as residue, etc.) seem inadequate in biology. The essential characteristic of the living thing is, in fact, that of having a history: that is, of being the concrete trace of a memory. (...) Making an epistemology of the living thing (and not of the inert) means identifying new categories which, being radically antithetical to disembodied notions like that of program and information, take account of the unpredictability and creativity which time introduces. This essay aims to bring some of these fundamental categories into focus. (shrink)