Explanation 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)

(This version was submitted to Behavioral and Brain Science. A revised version was published by Biological Theory) Estimates of autism’s incidence increased 5-10 fold in ten years, an increase which cannot be genetic. Though many mutations are associated with autism, no mutation seems directly to cause autism. We need to find the direct cause. Complexity science provides a new paradigm - confirmed in biology by extensive hard data. Both the body and the personality are complex dynamic systems which spontaneously self-organize (...) from simple dynamic systems. Autism may therefore be caused by the failure of a simple dynamic system. We know that infants who cannot track their mother’s face often become autistic, that eye-contact initiates intersubjectivity which is blocked in autism, and that the infant-mother pair seems designed to promote eye-contact, as does the eye’s appearance. This author earlier proposed that failure of eye-contact might directly cause autism and that early non-maternal childcare, including television/video, would therefore be statistically linked to autism. Waldman et al. (2008; 2006) recently proved that autism is strongly linked to precipitation (indoor activity) and to the introduction of cable. The most plausible explanation? Early exposure to television/video is linked to autism. Furthermore a normal developmental cascade (blocked in autism) has been deciphered: (a) Infant-mother eye-contact triggers increased maternal attention. (b) Early maternal attention permanently increases not only baseline vasopressin but also that oxytocin release which is triggered by subsequent maternal attention. (c) Vasopressin and oxytocin promote face recognition, gazing-at-the-eyes, emotion recognition, and social bonding. The eye-contact hypothesis suggests a clinical study addressing prevention: recruit prospective parents who agree to curtail television/video/computer/wi-fi in their families; measure autism’s incidence in their children. (shrink)

Abstract: This paper argues that a central explanatory role for the concept of Umwelt in theoretical biology is to be found in developmental biology, in particular in the effort to understand development as a goal-directed and adaptive process that is controlled by the organism itself. I will reach this conclusion in two (interrelated) ways. The first is purely theoretical and relates to the current scenario in the philosophy of biology. Challenging neo-Darwinism requires a new understanding of the various components involved (...) in natural selection processes. An important prerequisite for the explanation is the ability to understand development in a teleological way. Here, the concept of Umwelt plays a crucial role: if organisms are responsible for generating adaptive variation in specific environments, we need a theory that explains the context-dependent nature of adaptively oriented processes. The Umwelt is thus a central element in determining the goal that an adaptive process pursues. The second path in my analysis also has a historical dimension. I will present Karl Ernst von Baer’s reflections on teleological development and his influence on von Uexküll's thinking. I will present various ideas developed by von Baer, such as the distinction between Ziel and Zweck and the use of musical metaphors, which can help to understand development teleologically and give von Uexküll’s theory a central place in this framework. (shrink)

Various understandings and definitions of time will be reviewed. The nature and structure of time will be reviewed and the concepts of time and passage of time will be refreshed. The fundamental role played by energy and four natural forces in the actions, reactions and interactions concerning matter, anti-matter, energy in space and time will be critically analyzed. The reality how time is constructed during the construction of materials will be presented and discussed. The classical and quantum ideas in this (...) regard will be comprehensively studied. How these ideas will give us a fresh insight about the nature, structure and role of time in the construction of materials through natural scientific and manmade processes will be highlighted. The relations among matter, anti-matter, energy and time will be freshly stated. The milli-, micro-, nano, pico-, femto-, atto-times will be qualitatively analyzed considering physical, inorganic, organic and bio-materials and their construction and structure. The physics of timelessness also will be put forward. -/- . (shrink)

A formal model of the processes of digestion in a hypothetical cell is developed and discussed as a case study of how the threefold logic of Peircean semiotics works within Rosen’s paradigm of relational ontology. The formal model is used to demonstrate several fundamental differences between a relational description of biological processes and a mechanistic description. The formal model produces a logic of embodied generalization that is mediated and determined by the cell through its interactions with the environment. Specifically, the (...) synchronization of the functions of pattern recognition and semantic attribution results in an open and adaptive learning system that is stabilized by a hermeneutical circle. The relational principles of biosemiotics demonstrated through this case study are applicable to other biological systems, as well as to the relational ontology of systems theory, artificial intelligence systems, and relativistic quantum theory. (shrink)

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

Causal selection has to do with the distinction we make between background conditions and “the” true cause or causes of some outcome of interest. A longstanding consensus in philosophy views causal selection as lacking any objective rationale and as guided, instead, by arbitrary, pragmatic, and non-scientific considerations. I argue against this position in the context of causal selection for disease traits. In this domain, causes are selected on the basis of the type of causal control they exhibit over a disease (...) of interest. My analysis clarifies the principled rationale that guides this selection and how it involves both pragmatic and objective considerations, which have been overlooked in the extant literature. (shrink)

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)

Causal selection is the task of picking out, from a field of known causally relevant factors, some factors as elements of an explanation. The Causal Parity Thesis in the philosophy of biology challenges the usual ways of making such selections among different causes operating in a developing organism. The main target of this thesis is usually gene centrism, the doctrine that genes play some special role in ontogeny, which is often described in terms of information-bearing or programming. This paper is (...) concerned with the attempt of confronting the challenge coming from the Causal Parity Thesis by offering principles of causal selection that are spelled out in terms of an explicit philosophical account of causation, namely an interventionist account. I show that two such accounts that have been developed, although they contain important insights about causation in biology, nonetheless fail to provide an adequate reply to the Causal Parity challenge: Ken Waters's account of actual-difference making and Jim Woodward's account of causal specificity. A combination of the two also doesn't do the trick, nor does Laura Franklin-Hall's account of explanation (in this volume). We need additional conceptual resources. I argue that the resources we need consist in a special class of counterfactual conditionals, namely counterfactuals the antecedents of which describe biologically normal interventions. (shrink)

After Wesley Salmon’s causal-mechanical stance on explanation in the 1980s, the ontic-epistemic debate of scientific explanations appeared to be resolved in the philosophy of science. However, since the twenty-first century, this debate has been rekindled among philosophers who focus on mechanistic explanations. Nevertheless, its issues have evolved, necessitating scrutiny of the new trends in this debate and a comparison with the original controversy between Carl Hempel and Salmon. The primary objective of this paper is to elucidate three categorical dimensions in (...) the ontic-epistemic debates, spanning from the original to the recent controversies. Subsequently, it will explore why the conception of explanation is linked to representations, what conditions are necessary for linguistic expressions to be explanatory, and what roles norms play in explanation. Consequently, contrary to the common stereotype, it will be argued that mechanistic explanations are more likely to be epistemic rather than ontic. (shrink)

The paradoxical phenomena of hyperthermia-induced vasoconstriction, hyperthermia- induced hypothermia, and hyperthermia induced arterial vasoconstriction have been observed in animal heatstroke clinical case studies. We attempt to explain the basic mechanism behind such findings in terms of the principle of body heat conservation and natural countermeasure against heat exposure through reduction in the extent of vascular surface area exposed. One study which examined the outcome of heating a rabbit carotid artery produced graded vasoconstriction which is proportional to temperature increase. These interesting (...) results pointed out a spontaneous physiological counteractive measure to minimize organ and/or arterial surface area heat exposure through vasoconstriction which might otherwise prompt excessive heat gain from the ambient environment, or vasodilation, should it occur. When a blood vessel or artery constricts through smooth muscle activation, the amount of vascular surface area being exposed, whether to heat that is external from or internal within the body, is reduced. Since such vasoconstriction is proportional to temperature increase, the speed or rate at which this constriction responds and therefore, the extent of vascular surface area being reduced, may be drastic with extreme means of bodily cooling under a heat wave environment, such as whole-body cold-water bath or shower. The reason being extreme vasoconstriction of both cerebral and peripheral blood vessels, which may result in increased intravascular pressure due to intravascular spatial volume decrease and as an above study concluded, cerebral blood flow decreases and ischemia brain damage. (shrink)

We provide three innovations to recent debates about whether topological or “network” explanations are a species of mechanistic explanation. First, we more precisely characterize the requirement that all topological explanations are mechanistic explanations and show scientific practice to belie such a requirement. Second, we provide an account that unifies mechanistic and non-mechanistic topological explanations, thereby enriching both the mechanist and autonomist programs by highlighting when and where topological explanations are mechanistic. Third, we defend this view against some powerful mechanist objections. (...) We conclude from this that topological explanations are autonomous from their mechanistic counterparts. (shrink)

Millikan’s (1984. Language, Thought, and Other Biological Categories: New Foundations for Realism. MIT Press) selected effects theory of functions states that functions are effects for which the ancestors of a trait were selected for. As the function is an effect a thing’s ancestors produced, only things that are reproductions in some sense can have functions. Against this reproduction requirement, Garson (2019. What Biological Functions Are and Why They Matter. Cambridge University Press) argues that not only processes of differential reproduction but (...) also processes of differential persistence can lead to new functions. Since such “persistence functions” have the same explanatory power as traditional selected effects functions, selected effects theorists should include them in their theory. In this paper, I will defend Millikan’s theory against this argument. I will show that the proponents of the generalized theory have yet to provide a working notion of populations that avoids a liberality problem. Further, I will argue that persistence functions are at best a marginal case of functions due to their restricted explanatory power. (shrink)

Recent accounts of teleological naturalism hold that organisms are intrinsically goaldirected entities. We argue that supporters and critics of this view have ignored the ways in which it is used to address quite different problems. One problem is about biology and concerns whether an organism-centered account of teleological ascriptions would improve our descriptions and explanations of biological phenomena. This is different from the philosophical problem of how naturalized teleology would affect our conception of nature, and of ourselves as natural beings. (...) The neglect of this metatheoretic distinction has made it difficult to understand the criteria we should use for evaluating proposals to naturalize teleology. We argue that a clearer distinction between scientific and philosophical contexts shows that we need more than one set of criteria for evaluating proposals to naturalize teleology, and that taking these into account might advance or dissolve recurring debates in the literature. (shrink)

We characterize a type of functional explanation that addresses why a homologous trait originating deep in the evolutionary history of a group remains widespread and largely unchanged across the group’s lineages. We argue that biologists regularly provide this type of explanation when they attribute conserved functions to phenotypic and genetic traits. The concept of conserved function applies broadly to many biological domains, and we illustrate its importance using examples of molecular sequence alignments at the intersection of evolution and cell biology. (...) We use these examples to show how the study of conserved functions can integrate knowledge of a trait’s causal effects on fitness and its history of natural selection without invoking adaptation. We also show how conserved function provides a novel basis for addressing objections against evolutionary functions raised by Robert Cummins. (shrink)

Organization figures centrally in the understanding of biological systems advanced by both new mechanists and proponents of the autonomy framework. The new mechanists focus on how components of mechanisms are organized to produce a phenomenon and emphasize productive continuity between these components. The autonomy framework focuses on how the components of a biological system are organized in such a way that they contribute to the maintenance of the organisms that produce them. In this paper we analyze and compare these two (...) accounts of organization and argue that understanding biological organisms as cohesively integrated systems benefits from insights from both. To bring together the two accounts, we focus on the notions of control and regulation as bridge concepts. We start from a characterization of biological mechanisms in terms of constraints and focus on a specific type of mechanism, control mechanisms, that operate on other mechanisms on the basis of measurements of variables in the system and its environment. Control mechanisms are characterized by their own set of constraints that enable them to sense conditions, convey signals, and effect changes on constraints in the controlled mechanism. They thereby allow living organisms to adapt to internal and external variations and to coordinate their parts in such a manner as to maintain viability. Because living organisms contain a vast number of control mechanisms, a central challenge is to understand how they are themselves organized. With the support of examples from both unicellular and multicellular systems we argue that control mechanisms are organized heterarchically, and we discuss how this type of control architecture can, without invoking top-down and centralized forms of organizations, succeed in coordinating internal activities of organisms. (shrink)

Living organisms act as integrated wholes to maintain themselves. Individual actions can each be explained by characterizing the mechanisms that perform the activity. But these alone do not explain how various activities are coordinated and performed versatilely. We argue that this depends on a specific type of mechanism, a control mechanism. We develop an account of control by examining several extensively studied control mechanisms operative in the bacterium E. coli. On our analysis, what distinguishes a control mechanism from other mechanisms (...) is that it relies on measuring one or more variables, which results in setting constraints in the control mechanism that determine its action on flexible constraints in other mechanisms. In the most basic arrangement, the measurement process directly determines the action of the control mechanism, but in more complex arrangements signals mediate between measurements and effectors. This opens the possibility of multiple responses to the same measurement and responses based on multiple measurements. It also allows crosstalk, resulting in networks of control mechanisms. Such networks integrate the behaviors of the organism but also present a challenge in tailoring responses to particular measurements. We discuss how integrated activity can still result in differential, versatile, responses. (shrink)

This chapter provides a systematic overview of topological explanations in the philosophy of science literature. It does so by presenting an account of topological explanation that I (Kostić and Khalifa 2021; Kostić 2020a; 2020b; 2018) have developed in other publications and then comparing this account to other accounts of topological explanation. Finally, this appraisal is opinionated because it highlights some problems in alternative accounts of topological explanations, and also it outlines responses to some of the main criticisms raised by the (...) so-called new mechanists. (shrink)

Over the last fifteen years, an ambitious explanatory framework has been proposed to unify explanations across biology and cognitive science. Active inference, whose most famous tenet is the free energy principle, has inspired excitement and confusion in equal measure. Here, we lay the ground for proper critical analysis of active inference, in three ways. First, we give simplified versions of its core mathematical models. Second, we outline the historical development of active inference and its relationship to other theoretical approaches. Third, (...) we describe three different kinds of claim -- labelled mathematical, empirical and general -- routinely made by proponents of the framework, and suggest dialectical links between them. Overall, we aim to increase philosophical understanding of active inference so that it may be more readily evaluated. -/- This the final submitted version of the Introduction to the Topical Collection "The Free Energy Principle: From Biology to Cognition", forthcoming in Biology & Philosophy. (shrink)

According to the current scientific paradigm, what we call ‘life’, ‘mind’, and ‘consciousness’ are considered epiphenomenal occurrences, or emergent properties or functions of matter and energy. Science does not associate these with an inherent and distinct existence beyond a materialistic/energetic conception. ‘Life’ is a word pointing at cellular and multicellular processes forming organisms capable of specific functions and skills. ‘Mind’ is a cognitive ability emerging from a matrix of complex interactions of neuronal processes, while ‘consciousness’ is an even more elusive (...) concept, deemed a subjective epiphenomenon of brain activity. Historically, however, this has not always been the case, even in the scientific and academic context. Several prominent figures took vitalism seriously, while some schools of Western philosophical idealism and Eastern traditions promoted conceptions in which reality is reducible to mind or consciousness rather than matter. We will argue that current biological sciences did not falsify these alternative paradigms and that some forms of vitalism could be linked to some forms of idealism if we posit life and cognition as two distinct aspects of consciousness preeminent over matter. However, we will not argue in favor of vitalistic and idealistic conceptions. Rather, contrary to a physicalist doctrine, these were and remain coherent worldviews and cannot be ruled out by modern science. (shrink)

Neo‐Aristotelian ethical naturalism purports to show that moral evaluation of human action and character is an evaluation of natural goodness—a kind of evaluation that applies to living things in virtue of their nature and based on their form of life. The standard neo‐Aristotelian view defines natural goodness by way of generic statements describing the natural history, or the ‘characteristic’ life, of a species. In this paper, I argue that this conception of natural goodness commits the neo‐Aristotelian view to a problematic (...) anti‐individualism that results in the wrong assessment of individuals with uniquely adaptive adjustments. I then offer an alternative account of natural goodness that avoids this problem. Instead of relying on generic statements about a species, my account defines natural goodness based on counterfactual conditionals describing the modal properties of a single individual. I argue that this modal‐explanatory account gives a conception of natural goodness that is more intuitively plausible and better suited to capture the diversity and plasticity distinctive of life. (shrink)

Central to vaccination-induced responses, antibodies are suggested by Vaz to operate as observer-dependent entities that owe their status to categorization schemes of immunologists. Inspired by color research by Maturana, he argues that antibodies should be distinguished from immunoglobulins, which unlike the former can be considered as constituents of structural dynamics of an organism, products of millions of years of evolution. However, a deeper understanding of the historical roots of the concept of immunoglobulin and associated “languaging” and naming processes reveals that (...) immunoglobulins, as much as antibodies, are contingent on conceptual schemes of immunology. (shrink)

There is a deep-seated neopositivist view which regards the language of science as a neutral medium of communication, radically different from indirect symbolic forms of discourse characteristic of arts and humanities. But naturalists, like poets and social scientists, also draw on the dominant images in their culture to organize their thoughts and simplify complex concepts. By conceptualizing one thing in terms of another, metaphors in science not only aid mutual communication between researchers but also structure their understanding of experience and (...) reality. Too transparent to be noticed and critically analyzed within the framework of science itself, metaphors act as lenses, making selected aspects of complex phenomena visible to study and investigation (Reynolds 2018). By linking two seemingly unrelated ideas, for example, those of a machine and DNA replication, metaphors establish new interactions of meaning evoking shared associated connotations between these interacting concepts (Black 1962). This, in turn, may not only transform the perception of a target domain but also open up new prospects for experimental and interpretative avenues. Understanding Metaphors by Andrew Reynolds draws on this vision of metaphors as indispensable tools of scientific thinking to elucidate their role in the life sciences. (shrink)

The recent literature on causality has seen the introduction of several distinctions within causality, which are thought to be important for understanding the widespread scientific practice of focusing causal explanations on a subset of the factors that are causally relevant for a phenomenon. Concepts used to draw such distinctions include, among others, stability, specificity, proportionality, or actual-difference making. In this contribution, I propose a new distinction that picks out an explanatorily salient class of causes in biological systems. Some select causes (...) in complex biological systems, I argue, have the property of enabling coherent causal control of these systems. Examples of such control variables include hormones and other signaling molecules, e.g., TOR (target of rapamycin), morphogens or the products of homeotic selector genes in embryonic pattern formation. I propose an analysis of this notion based on concepts borrowed from causal graph theory. (shrink)

This afterword to Species and Beyond provides some reflections on species, with special attention to what I think the most significant developments have been in the thinking of biologists and philosophers working on species over the past 25 years, as well as some bad jokes.

Teleology has a complicated history in the biological sciences. Some have argued that Darwin’s theory has allowed biology to purge itself of teleological explanations. Others have been content to retain teleology and to treat it as metaphorical, or have sought to replace it with less problematic notions like teleonomy. And still others have tried to naturalize it in a way that distances it from the vitalism of the nineteenth century, focusing on the role that function plays in teleological explanation. No (...) consensus has seemed possible in this debate. This paper takes a different approach. It argues that teleology is a perfectly acceptable scientific notion, but that the debate took an unfortunate misstep some 2300 years ago, one that has confused things ever since. The misstep comes in the beginning of Aristotle’s Physics when a distinction is made between two types of teleological explanation. One type pertains to artifacts while the other pertains to entities in nature. For Aristotle, artifacts are guided by something external to themselves, human intentions, while natural entities are guided by an internal nature. We aim to show that there is, in fact, only one type of legitimate teleological explanation, what Aristotle would have considered a variant of an artifact model, where entities are guided by external fields. We begin with an analysis of the differences between the two types of explanation. We then examine some evidence in Aristotle’s biological works suggesting that on account of his natural-artifactual distinction, he encountered difficulties in trying to provide teleological accounts of spontaneous generation. And we show that it is possible to resolve these difficulties with a more robust version of an artifact model of teleology, in other words, with an externalist teleology. This is McShea’s model, in which goal-directed entities are guided by a nested series of upper-level fields. To explain teleological behavior, this account invokes only external physical forces rather than mysterious internal natures. We then consider how field theory differs from other efforts to naturalize teleology in biology. And finally, we show how the account enables us to grapple with certain difficult cases – genes and intentions – where, even in biology today, the temptation to posit internal natures remains strong. (shrink)

This paper discusses the epistemic status of biology from the standpoint of the systemic approach to living systems based on the notion of biological autonomy. This approach aims to provide an understanding of the distinctive character of biological systems and this paper analyses its theoretical and epistemological dimensions. The paper argues that, considered from this perspective, biological systems are examples of emergent phenomena, that the biological domain exhibits special features with respect to other domains, and that biology as a discipline (...) employs some core concepts, such as teleology, function, regulation among others, that are irreducible to those employed in physics and chemistry. It addresses the claim made by Jacques Monod that biology as a science is marginal. It argues that biology is general insofar as it constitutes a paradigmatic example of complexity science, both in terms of how it defines the theoretical object of study and of the epistemology and heuristics employed. As such, biology may provide lessons that can be applied more widely to develop an epistemology of complex systems. (shrink)

The new mechanists and the autonomy approach both aim to account for how biological phenomena are explained. One identifies appeals to how components of a mechanism are organized so that their activities produce a phenomenon. The other directs attention towards the whole organism and focuses on how it achieves self-maintenance. This paper discusses challenges each confronts and how each could benefit from collaboration with the other: the new mechanistic framework can gain by taking into account what happens outside individual mechanisms, (...) while the autonomy approach can ground itself in biological research into how the actual components constituting an autonomous system interact and contribute in different ways to realize and maintain the system. To press the case that these two traditions should be constructively integrated we describe how three recent developments in the autonomy tradition together provide a bridge between the two traditions: (1) a framework of work and constraints, (2) a conception of function grounded in the organization of an autonomous system, and (3) a focus on control. (shrink)

One of the aims of the encyclical "Laudato Si’" is to help us “marvel at the manifold connections existing among creatures”, to show how we are also involved, and to motivate us thereby to care for our common home. Are there new dimensions of beauty available to us today because of recent advances in biology? In this paper I seek to answer this question by first recalling the basic criteria for beauty, as expressed by Aristotle and Aquinas, and then evaluating (...) their applicability as regards three ways in which some prominent twentieth century philosophers of biology have sought to overcome the limitations of reductionism. The overall argument refers especially to the works of Jakob von Uexküll and Georges Canguilhem. The results indicate that harmony, proportion, and integrity in the natural order should be more evident than ever before, especially as regards the way the organism and its environment codetermine each other. This insight allows a deeper appreciation of the message of "Laudato Si’". (shrink)

The free-energy principle states that all systems that minimize their free energy resist a tendency to physical disintegration. Originally proposed to account for perception, learning, and action, the free-energy principle has been applied to the evolution, development, morphology, anatomy and function of the brain, and has been called a postulate, an unfalsifiable principle, a natural law, and an imperative. While it might afford a theoretical foundation for understanding the relationship between environment, life, and mind, its epistemic status is unclear. Also (...) unclear is how the free-energy principle relates to prominent theoretical approaches to life science phenomena, such as organicism and mechanism. This paper clarifies both issues, and identifies limits and prospects for the free-energy principle as a first principle in the life sciences. (shrink)

Causation has multiple distinct meanings in genetics. One reason for this is meaning slippage between two concepts of the gene: Mendelian and molecular. Another reason is that a variety of genetic methods address different kinds of causal relationships. Some genetic studies address causes of traits in individuals, which can only be assessed when single genes follow predictable inheritance patterns that reliably cause a trait. A second sense concerns the causes of trait differences within a population. Whereas some single genes can (...) be said to cause population-level differences, most often these claims concern the effects of many genes. Polygenic traits can be understood using heritability estimates, which estimate the relative influences of genetic and environmental differences to trait differences within a population. Attempts to understand the molecular mechanisms underlying polygenic traits have been developed, although causal inference based on these results remains controversial. Genetic variation has also recently been leveraged as a randomizing factor to identify environmental causes of trait differences. This technique—Mendelian randomization—offers some solutions to traditional epidemiological challenges, although it is limited to the study of environments with known genetic influences. (shrink)

Mathematics is often taken to play one of two roles in the empirical sciences: either it represents empirical phenomena or it explains these phenomena by imposing constraints on them. This article identifies a third and distinct role that has not been fully appreciated in the literature on applicability of mathematics and may be pervasive in scientific practice. I call this the “bridging” role of mathematics, according to which mathematics acts as a connecting scheme in our explanatory reasoning about why and (...) how two different descriptions of an empirical phenomenon relate to each other. I discuss two bridging roles appearing in biological and physical explanations. (shrink)

Endocrinologists apply the idea of feedback loops to explain how hormones regulate certain bodily functions such as glucose metabolism. In particular, feedback loops focus on the maintenance of the plasma concentrations of glucose within a narrow range. Here, we put forward a different, organicist perspective on the endocrine regulation of glycaemia, by relying on the pivotal concept of closure of constraints. From this perspective, biological systems are understood as organized ones, which means that they are constituted of a set of (...) mutually dependent functional structures acting as constraints, whose maintenance depends on their reciprocal interactions. Closure refers specifically to the mutual dependence among functional constraints in an organism. We show that, when compared to feedback loops, organizational closure can generate much richer descriptions of the processes and constraints at play in the metabolism and regulation of glycaemia, by making explicit the different hierarchical orders involved. We expect that the proposed theoretical framework will open the way to the construction of original mathematical models, which would provide a better understanding of endocrine regulation from an organicist perspective. (shrink)

I argue for the usefulness of the evolutionary kind of biological individual.

This dissertation argues that cognition is a kind of natural agency. Natural agency is the capacity that certain systems have to act in accordance with their own norms. Natural agents are systems that bias their repertoires in response to affordances in the pursuit of their goals. Cognition is a special mode of this general phenomenon. Cognitive systems are agents that have the additional capacity to actively take their worlds to be certain ways, regardless of whether the world is really that (...) way. In this way, cognitive systems are desituated. Desituatedness is the root of specifically cognitive capacities for representation and abstraction. There are two main reasons why this view needs defending. First, natural agency is typically viewed as incompatible with natural science because it is committed to a teleological mode of explanation. Second, cognition is typically held to be categorically distinct from natural agency. This dissertation argues against both of these views. It argues against the incompatibility of agency and natural science by demonstrating that systems biology, general systems theory, and sciences that deal with complex systems have typically underappreciated conceptual and theoretical resources for grounding agency in the causal structure of the world. These conceptual resources do not, however, reduce agency to systems theory because the normativity inherent in agency demands descriptive resources beyond those of even the most sophisticated systems theory. It argues against the categorical difference between natural agency and cognition by pointing out that separating cognition from a richer web of situated, ecologically embedded relations between the agent and the world generates the frame problem, which is an insuperable obstacle to making cognition that is sufficiently responsive to the complexity of the world. Rooting cognition in natural agency is a more robust empirical bet for theorizing cognition and artificial intelligence. (shrink)

The mantra that "the best way to predict the future is to invent it" (attributed to the computer scientist Alan Kay) exemplifies some of the expectations from the technical and innovative sides of biomedical research at present. However, for technical advancements to make real impacts both on patient health and genuine scientific understanding, quite a number of lingering challenges facing the entire spectrum from protein biology all the way to randomized controlled trials should start to be overcome. The proposal in (...) this chapter is that philosophy is essential in this process. By reviewing select examples from the history of science and philosophy, disciplines which were indistinguishable until the mid-nineteenth century, I argue that progress toward the many impasses in biomedicine can be achieved by emphasizing theoretical work (in the true sense of the word 'theory') as a vital foundation for experimental biology. Furthermore, a philosophical biology program that could provide a framework for theoretical investigations is outlined. (shrink)

Though biologists identify individuals as ‘male’ or ‘female’ across a broad range of animal species, the particular traits exhibited by males and females can vary tremendously. This diversity has led some to conclude that cross-animal sexes (males, or females, of whatever animal species) have “little or no explanatory power” (Dupré 1986: 447) and, thus, are not natural kinds in any traditional sense. This essay will explore considerations for and against this conclusion, ultimately arguing that the animal sexes, properly understood, are (...) “historical explanatory kinds”: groupings that can be scientifically significant even while their members differ radically in their current properties and particular histories. Whether this makes them full-fledged natural kinds is a question I take up at the very end. (shrink)

In this paper, I present a general theory of topological explanations, and illustrate its fruitfulness by showing how it accounts for explanatory asymmetry. My argument is developed in three steps. In the first step, I show what it is for some topological property A to explain some physical or dynamical property B. Based on that, I derive three key criteria of successful topological explanations: a criterion concerning the facticity of topological explanations, i.e. what makes it true of a particular system; (...) a criterion for describing counterfactual dependencies in two explanatory modes, i.e. the vertical and the horizontal; and, finally, a third perspectival one that tells us when to use the vertical and when to use the horizontal mode. In the second step, I show how this general theory of topological explanations accounts for explanatory asymmetry in both the vertical and horizontal explanatory modes. Finally, in the third step, I argue that this theory is universally applicable across biological sciences, which helps to unify essential concepts of biological networks. (shrink)

Mechanistic explanations are often said to explain because they reveal the causal structure of the world. Conversely, dynamical models supposedly lack explanatory power because they do not describe causal structure. The only way for dynamical models to produce causal explanations is via the 3M criterion: the model must be mapped onto a mechanism. This framing of the situation has become the received view around the viability of dynamical explanation. In this paper, I argue against this position and show that dynamical (...) models can themselves reveal causal structure and consequently produce nonmechanistic, dynamical explanations. Taking the example of cell fates from systems biology, I show how dynamical models, and specifically the attractor landscapes they describe, identify the causes of cell differentiation and explain why cells select particular fates. These dynamical features of the system better fit Woodward’s (2010, 2018) criteria of specificity and proportionality and make them the best candidate causes of cell fates than mechanisms. I also show how these causes are irreducible and inaccessible to mechanistic models, making 3M unworkable and counterproductive in this case. Dynamical models can reveal dynamical causes and thereby provide causal explanations. (shrink)

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)

One of biology's fundamental aims is to generate understanding of the living world around—and within—us. In this chapter, I aim to provide a relatively nonpartisan discussion of the nature of explanation in biology, grounded in widely shared philosophical views about scientific explanation. But this discussion also reflects what I think is important for philosophers and biologists alike to appreciate about successful scientific explanations, so some points will be controversial, at least among philosophers. I make three main points: (1) causal relationships (...) and broad patterns have often been granted importance to scientific explanations, and they are in fact both important; (2) some explanations in biology cite the components of or processes in systems that account for the systems’ features, whereas other explanations feature large-scale or structural causes that influence a system; and (3) there can be multiple different explanations of a given biological phenomenon, explanations that respond to different research aims and can thus be compatible with one another even when they may seem to disagree. (shrink)

This paper adds to the philosophical literature on mechanistic explanation by elaborating two related explanatory functions of idealisation in mechanistic models. The first function involves explaining the presence of structural/organizational features of mechanisms by reference to their role as difference-makers for performance requirements. The second involves tracking counterfactual dependency relations between features of mechanisms and features of mechanistic explanandum phenomena. To make these functions salient, we relate our discussion to an exemplar from systems biological research on the mechanism for countering (...) heat shock—the heat shock response system—in Escherichia coli bacteria. This research also reinforces a more general lesson: ontic constraint accounts in the literature on mechanistic explanation provide insufficiently informative normative appraisals of mechanistic models. We close by outlining an alternative view on the explanatory norms governing mechanistic representation. (shrink)

In this article I give a critical evaluation of the use and limitations of null-model-based hypothesis testing as a research strategy in the biological sciences. According to this strategy, the null model based on a randomization procedure provides an appropriate null hypothesis stating that the existence of a pattern is the result of random processes or can be expected by chance alone, and proponents of other hypotheses should first try to reject this null hypothesis in order to demonstrate their own (...) hypotheses. Using as an example the controversy over the use of null hypotheses and null models in species co-occurrence studies, I argue that null-model-based hypothesis testing fails to work as a proper analog to traditional statistical null-hypothesis testing as used in well-controlled experimental research, and that the random process hypothesis should not be privileged as a null hypothesis. Instead, the possible use of the null model resides in its role of providing a way to challenge scientists’ commonsense judgments about how a seemingly unusual pattern could have come to be. Despite this possible use, null-model-based hypothesis testing still carries certain limitations, and it should not be regarded as an obligation for biologists who are interested in explaining patterns in nature to first conduct such a test before pursuing their own hypotheses. (shrink)

Explaining the behaviour of ecosystems is one of the key challenges for the biological sciences. Since 2000, new-mechanicism has been the main model to account for the nature of scientific explanation in biology. The universality of the new-mechanist view in biology has been however put into question due to the existence of explanations that account for some biological phenomena in terms of their mathematical properties (mathematical explanations). Supporters of mathematical explanation have argued that the explanation of the behaviour of ecosystems (...) is usually provided in terms of their mathematical properties, and not in mechanistic terms. They have intensively studied the explanation of the properties of ecosystems that behave following the rules of a non-random network. However, no attention has been devoted to the study of the nature of the explanation in those that form a random network. In this paper, we cover that gap by analysing the explanation of the stability behaviour of the microbiome recently elaborated by Coyte and colleagues, to determine whether it fits with the model of explanation suggested by the new-mechanist or by the defenders of mathematical explanation. Our analysis of this case study supports three theses: (1) that the explanation is not given solely in terms of mechanisms, as the new-mechanists understand the concept; (2) that the mathematical properties that describe the system play an essential explanatory role, but they do not exhaust the explanation; (3) that a non-previously identified appeal to the type of interactions that the entities in the network can exhibit, as well as their abundance, is also necessary for Coyte and colleagues’ account to be fully explanatory. From the combination of these three theses we argue for the necessity of an integrative pluralist view of the nature of behaviour explanation when this is given by appealing to the existence of a random network. (shrink)

The so-called “Baldwin Effect” has been studied for years in the fields of Artificial Life, Cognitive Science, and Evolutionary Theory across disciplines. This idea is often conflated with genetic assimilation, and has raised controversy in trans-disciplinary scientific discourse due to the many interpretations it has. This paper revisits the “Baldwin Effect” in Baldwin’s original spirit from a joint historical, theoretical and experimental approach. Social Heredity – the inheritance of cultural knowledge via non-genetic means in Baldwin’s term – is also taken (...) into consideration. I shall argue that the Baldwin Effect can occur via social heredity without necessity for genetic assimilation. Computational experiments are carried out to show that when social heredity is permitted with high fidelity, there is no need for the assimilation of acquired characteristics; instead the Baldwin Effect occurs as promoting more plasticity to facilitate future intelligence. The role of mind and intelligence in evolution and its implications in an extended synthesis of evolution are briefly discussed. (shrink)

We provide a new perspective on the relation between the space of description of an object and the appearance of novelties. One of the aims of this perspective is to facilitate the interaction between mathematics and historical sciences. The definition of novelties is paradoxical: if one can define in advance the possibles, then they are not genuinely new. By analyzing the situation in set theory, we show that defining generic (i.e., shared) and specific (i.e., individual) properties of elements of a (...) set are radically different notions. As a result, generic and specific definitions of possibilities cannot be conflated. We argue that genuinely stating possibilities requires that their meaning has to be made explicit. For example, in physics, properties playing theoretical roles are generic; then, generic reasoning is sufficient to define possibilities. By contrast, in music, we argue that specific properties matter, and generic definitions become insufficient. Then, the notion of new possibilities becomes relevant and irreducible. In biology, among other examples, the generic definition of the space of DNA sequences is insufficient to state phenotypic possibilities even if we assume complete genetic determinism. The generic properties of this space are relevant for sequencing or DNA duplication, but they are inadequate to understand phenotypes. We develop a strong concept of biological novelties which justifies the notion of new possibilities and is more robust than the notion of changing description spaces. These biological novelties are not generic outcomes from an initial situation. They are specific and this specificity is associated with biological functions, that is to say, with a specific causal structure. Thus, we think that in contrast with physics, the concept of new possibilities is necessary for biology. (shrink)

For many old and new mechanists, Mechanism is both a metaphysical position and a thesis about scientific methodology. In this paper we discuss the relation between the metaphysics of mechanisms and the role of mechanical explanation in the practice of science, by presenting and comparing the key tenets of Old and New Mechanism. First, by focusing on the case of gravity, we show how the metaphysics of Old Mechanism constrained scientific explanation, and discuss Newton’s critique of Old Mechanism. Second, we (...) examine the current mechanistic metaphysics, arguing that it is not warranted by the use of the concept of mechanism in scientific practice, and motivate a thin conception of mechanism (the truly minimal view), according to which mechanisms are causal pathways for a certain effect or phenomenon. Finally, we draw analogies between Newton’s critique of Old Mechanism and our thesis that the metaphysical commitments of New Mechanism are not necessary in order to illuminate scientific practice. (shrink)

In this paper we defend the view that mechanisms are underpinned by networks of difference-making relations. First, we distinguish and criticise two different kinds of arguments in favour of an activity-based understanding of mechanism: Glennan’s metaphysics- first approach and Illari and Williamson’s science-first approach. Second, we present an alternative difference-making view of mechanism and illustrate it by looking at the history of the case of scurvy prevention. We use the case of scurvy to argue that evidence for a mechanism just (...) is evidence for difference-making relations. (shrink)

Philippe Huneman has recently questioned the widespread application of mechanistic models of scientific explanation based on the existence of structural explanations, i.e. explanations that account for the phenomenon to be explained in virtue of the mathematical properties of the system where the phenomenon obtains, rather than in terms of the mechanisms that causally produce the phenomenon. Structural explanations are very diverse, including cases like explanations in terms of bowtie structures, in terms of the topological properties of the system, or in (...) terms of equilibrium. The role of mathematics in bowtie structured systems and in topologically constrained systems has recently been examined in different papers. However, the specific role that mathematical properties play in equilibrium explanations requires further examination, as different authors defend different interpretations, some of them closer to the new-mechanistic approach than to the structural model advocated by Huneman. In this paper, we cover this gap by investigating the explanatory role that mathematics play in Blaser and Kirschner’s nested equilibrium model of the stability of persistent long-term human-microbe associations. We argue that their model is explanatory because: i) it provides a mathematical structure in the form of a set of differential equations that together satisfy an ESS; ii) that the nested nature of the ESSs makes the explanation of host-microbe persistent associations robust to any perturbation; iii) that this is so because the properties of the ESS directly mirror the properties of the biological system in a non-causal way. The combination of these three theses make equilibrium explanations look more similar to structural explanations than to causal-mechanistic explanation. (shrink)

Optimality models are widely used in different parts of biology. Two important questions that have been asked about such models are: are they explanatory and, if so, what type of explanations do they offer? My concern in this paper is with the approach of Rice (2012, 2015) and Irvine (2015), who claim that these models provide non-causal explanations. I argue that there are serious problems with this approach and with the accounts of explanation it is intended to justify. The idea (...) behind this undertaking is to draw attention to an important issue associated with the recent pluralist stance on explanation: the rampant proliferation of theories of explanation. This proliferation supports a pluralist perspective on explanation, and pluralism encourages such a proliferation. But, if we are not careful about how we arrive at and how we justify new accounts of explanation — i.e., if we do not try to avoid the sort of problems discussed in this paper — we may end up trivializing the concept of explanation. (shrink)