Emergence is much discussed by both philosophers and scientists. But, as noted by Mitchell (2012), there is a significant gulf; philosophers and scientists talk past each other. We contend that this is because philosophers and scientists typically mean different things by emergence, leading us to distinguish being emergence and pattern emergence. While related to distinctions offered by others between, for example, strong/weak emergence or epistemic/ontological emergence (Clayton, 2004, pp. 9–11), we argue that the being vs. pattern distinction better captures what (...) the two groups are addressing. In identifying pattern emergence as the central concern of scientists, however, we do not mean that pattern emergence is of no interest to philosophers. Rather, we argue that philosophers should attend to, and even contribute to, discussions of pattern emergence. But it is important that this discussion be distinguished, not conflated, with discussions of being emergence. In the following section we explicate the notion of being emergence and show how it has been the focus of many philosophical discussions, historical and contemporary. In section 3 we turn to pattern emergence, briefly presenting a few of the ways it figures in the discussions of scientists (and philosophers of science who contribute to these discussions in science). Finally, in sections 4 and 5, we consider the relevance of pattern emergence to several central topics in philosophy of biology: the emergence of complexity, of control, and of goal-directedness in biological systems. (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)

Cattle farming is a traditional agricultural system that contributes to the rural economic, social, and cultural values of the communities. Cattle as common with other livestock, are affected by many diseases that cause mortality and economic losses. In many rural households, the use of plants and associated knowledge are popular for managing cattle diseases, especially in areas experiencing challenges with conventional veterinary medicine. Evidence on the documentation of indigenous knowledge and biological evaluation of plants used against cattle diseases remain understudied (...) and fragmented. The aim of the review is to collate and analyze the ethnoveterinary knowledge and biological evaluation of plants used against cattle diseases in South Africa. Different scientific databases were systematically explored to extract data from 37 eligible studies. A total of 310 medicinal plants from 81 families were used to treat 10 categories of cattle diseases across seven (7) provinces in South Africa. Leguminosae (Fabaceae), Compositae (Asteraceae), Asparagaceae, and Xanthorrhoeaceae were the most frequently used plant families. Common plant parts used were leaves and roots. Twenty-seven (27) combination remedies involving 2–6 plants were identified as treatment regimes against cattle diseases. Common preparation methods were infusion and decoction while the administration mode was predominantly unspecified (52%) while oral and topical contributed 26 and 22%, respectively. In terms of diseases, the most treated ones were general systems infection, reproduction disorders, and gastrointestinal problems. Currently, an estimated 21% of the 310 plants have been evaluated for diverse biological activities using relevant bioassays related to cattle diseases. Antibacterial activity remained the most studied biological activity. Evidence from the review revealed the significance of ethnoveterinary medicine against cattle diseases especially in rural areas of South Africa. Nevertheless, the use of plants for cattle diseases among other ethnic groups, particularly in the Northern Cape and Western Cape, remains understudied. (shrink)

I describe two traditions of philosophical accounts of evidence: one characterizes the notion in terms of signs of success, the other characterizes the notion in terms of conditions of success. The best examples of the former rely on the probability calculus, and have the virtues of generality and theoretical simplicity. The best examples of the latter describe the features of evidence which scientists appeal to in practice, which include general features of methods, such as quality and relevance, and general features (...) of evidence, such as patterns in data, concordance with other evidence, and believability of the evidence. Two infamous episodes from biomedical research help to illustrate these features. Philosophical characterization of these latter features—conditions of success—has the virtue of potential relevance to, and descriptive accuracy of, practices of experimental scientists. (shrink)

Modern life sciences research is increasingly relying on artificial intelligence (AI) approaches to model biological systems, primarily centered around the use of machine learning (ML) models. Although ML is undeniably useful for identifying patterns in large, complex data sets, its widespread application in biological sciences represents a significant deviation from traditional methods of scientific inquiry. As such, the interplay between these models and scientific understanding in biology is a topic with important implications for the future of scientific research, (...) yet it is a subject that has received little attention. Here, we draw from an epistemological toolkit to contextualize recent applications of ML in biological sciences under modern philosophical theories of understanding, identifying general principles that can guide the design and application of ML systems to model biological phenomena and advance scientific knowledge. We propose that conceptions of scientific understanding as information compression, qualitative intelligibility, and dependency relation modelling provide a useful framework for interpreting ML-mediated understanding of biological systems. Through a detailed analysis of two key application areas of ML in modern biological research – protein structure prediction and single cell RNA-sequencing – we explore how these features have thus far enabled ML systems to advance scientific understanding of their target phenomena, how they may guide the development of future ML models, and the key obstacles that remain in preventing ML from achieving its potential as a tool for biological discovery. Consideration of the epistemological features of ML applications in biology will improve the prospects of these methods to solve important problems and advance scientific understanding of living systems. (shrink)

The INBIOSA project brings together a group of experts across many disciplines who believe that science requires a revolutionary transformative step in order to address many of the vexing challenges presented by the world. It is INBIOSA’s purpose to enable the focused collaboration of an interdisciplinary community of original thinkers. This paper sets out the case for support for this effort. The focus of the transformative research program proposal is biology-centric. We admit that biology to date has been (...) more fact-oriented and less theoretical than physics. However, the key leverageable idea is that careful extension of the science of living systems can be more effectively applied to some of our most vexing modern problems than the prevailing scheme, derived from abstractions in physics. While these have some universal application and demonstrate computational advantages, they are not theoretically mandated for the living. A new set of mathematical abstractions derived from biology can now be similarly extended. This is made possible by leveraging new formal tools to understand abstraction and enable computability. [The latter has a much expanded meaning in our context from the one known and used in computer science and biology today, that is "by rote algorithmic means", since it is not known if a living system is computable in this sense (Mossio et al., 2009).] Two major challenges constitute the effort. The first challenge is to design an original general system of abstractions within the biological domain. The initial issue is descriptive leading to the explanatory. There has not yet been a serious formal examination of the abstractions of the biological domain. What is used today is an amalgam; much is inherited from physics (via the bridging abstractions of chemistry) and there are many new abstractions from advances in mathematics (incentivized by the need for more capable computational analyses). Interspersed are abstractions, concepts and underlying assumptions “native” to biology and distinct from the mechanical language of physics and computation as we know them. A pressing agenda should be to single out the most concrete and at the same time the most fundamental process-units in biology and to recruit them into the descriptive domain. Therefore, the first challenge is to build a coherent formal system of abstractions and operations that is truly native to living systems. Nothing will be thrown away, but many common methods will be philosophically recast, just as in physics relativity subsumed and reinterpreted Newtonian mechanics. -/- This step is required because we need a comprehensible, formal system to apply in many domains. Emphasis should be placed on the distinction between multi-perspective analysis and synthesis and on what could be the basic terms or tools needed. The second challenge is relatively simple: the actual application of this set of biology-centric ways and means to cross-disciplinary problems. In its early stages, this will seem to be a “new science”. This White Paper sets out the case of continuing support of Information and Communication Technology (ICT) for transformative research in biology and information processing centered on paradigm changes in the epistemological, ontological, mathematical and computational bases of the science of living systems. Today, curiously, living systems cannot be said to be anything more than dissipative structures organized internally by genetic information. There is not anything substantially different from abiotic systems other than the empirical nature of their robustness. We believe that there are other new and unique properties and patterns comprehensible at this bio-logical level. The report lays out a fundamental set of approaches to articulate these properties and patterns, and is composed as follows. -/- Sections 1 through 4 (preamble, introduction, motivation and major biomathematical problems) are incipient. Section 5 describes the issues affecting Integral Biomathics and Section 6 -- the aspects of the Grand Challenge we face with this project. Section 7 contemplates the effort to formalize a General Theory of Living Systems (GTLS) from what we have today. The goal is to have a formal system, equivalent to that which exists in the physics community. Here we define how to perceive the role of time in biology. Section 8 describes the initial efforts to apply this general theory of living systems in many domains, with special emphasis on crossdisciplinary problems and multiple domains spanning both “hard” and “soft” sciences. The expected result is a coherent collection of integrated mathematical techniques. Section 9 discusses the first two test cases, project proposals, of our approach. They are designed to demonstrate the ability of our approach to address “wicked problems” which span across physics, chemistry, biology, societies and societal dynamics. The solutions require integrated measurable results at multiple levels known as “grand challenges” to existing methods. Finally, Section 10 adheres to an appeal for action, advocating the necessity for further long-term support of the INBIOSA program. -/- The report is concluded with preliminary non-exclusive list of challenging research themes to address, as well as required administrative actions. The efforts described in the ten sections of this White Paper will proceed concurrently. Collectively, they describe a program that can be managed and measured as it progresses. (shrink)

While many different mechanisms contribute to the generation of spatial order in biological development, the formation of morphogenetic fields which in turn direct cell responses giving rise to pattern and form are of major importance and essential for embryogenesis and regeneration. Most likely the fields represent concentration patterns of substances produced by molecular kinetics. Short range autocatalytic activation in conjunction with longer range “lateral” inhibition or depletion effects is capable of generating such patterns (Gierer and Meinhardt, 1972). Non-linear (...) reactions are required, and mathematical criteria were derived to design molecular models capable of pattern generation. The classical embryological feature of proportion regulation can be incorporated into the models. The conditions are mathematically necessary for the simplest two-factor case, and are likely to be a fair approximation in multi-component systems in which activation and inhibition are systems parameters subsuming the action of several agents. Gradients, symmetric and periodic patterns, in one or two dimensions, stable or pulsing in time, can be generated on this basis. Our basic concept of autocatalysis in conjunction with lateral inhibition accounts for self-regulatory biological features, including the reproducible formation of structures from near-uniform initial conditions as required by the logic of the generation cycle. Real tissue form, for instance that of budding Hydra, may often be traced back to local curvature arising within an initially relatively flat cell sheet, the position of evagination being determined by morphogenetic fields. Shell theory developed for architecture may also be applied to such biological processes. (shrink)

The paper addresses the formation of striking patterns within originally near-homogenous tissue, the process prototypical for embryology, and represented in particularly purist form by cut sections of hydra regenerating, by internal reorganisation of the pre-existing tissue, a complete animal with head and foot. The essential requirements are autocatalytic, self-enhancing activation, combined with inhibitory or depletion effects of wider range – “lateral inhibition”. Not only de-novo-pattern formation, but also well known, striking features of developmental regulation such as induction, inhibition, and (...) proportion regulation can be explained on this basis. The theory provides a mathematical recipe for the construction of molecular models with criteria for the necessary non-linear interactions. It has since been widely applied to different developmental processes. (shrink)

This essay aims to expose the metaphysical underpinnings of enactivism. While enactivism relies heavily on rejecting the traditional mind-body problem by excluding the familiar thought experiments that favor phenomenal dualism, the crucial point that is overlooked is instead the brain-body problem, specifically the crucial interaction between the brain and the bodily limbs in their embodied activities of perception and cognition. If enactivism is correct, differences in sensory experience necessarily entail differences in embodied activity—this is the metaphysical core of enactivism, which (...) we think is entirely wrong. We will argue that a physical or biological body ("Körper") is configured or shaped into a perceptually living body ("Leib") by brain patterns and not by embodied activity or by the so-called sensorimotor contingencies. Undoubtedly, embodied actions influence sensory perception. However, since variations in embodied actions do not necessarily lead to variations in sensory experience, they are not metaphysically constitutive of these experiences (supervenience claim). (shrink)

Whether man is predisposed to lethal violence, ranging from homicide to warfare, and how that may have impacted human evolution, are among the most controversial topics of debate on human evolution. Although recent studies on the evolution of warfare have been based on various archaeological and ethnographic data, they have reported mixed results: it is unclear whether or not warfare among prehistoric hunter – gatherers was common enough to be a component of human nature and a selective pressure for the (...) evolution of human behaviour. This paper reports the mortality attributable to violence, and the spatio-temporal pattern of violence thus shown among ancient hunter–gatherers using skeletal evidence in prehistoric Japan (the Jomon period: 13000 cal BC–800 cal BC). Our results suggest that the mortality due to violence was low and spatio-temporally highly restricted in the Jomon period, which implies that violence including warfare in prehistoric Japan was not common. (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)

We present a technique for the analysis of pattern formation by a class of models for the formation of ocular dominance stripes in the striate cortex of some mammals. The method, which employs the adiabatic approximation to derive a set of ordinary differential equations for patterning modes, has been successfully applied to reaction-diffusion models for striped patterns [1]. Models of ocular dominance stripes have been studied [2,3] by computation, or by linearization of the model equations. These techniques do not (...) provide a rationale for the origin of the stripes. We show here that stripe formation is a non-linear property of the models. Our analysis indicates that stripe selection is closely linked to a property in the dynamics of the models which arises from a symmetry between ipsilateral and contralateral synapses to the visual cortex of a given hemisphere. (shrink)

The mathematical universe hypothesis is a theory that the physical universe is not merely described by mathematics, but is mathematics, specifically a mathematical structure. Our research provides evidence that the mathematical structure of the universe is biological in nature and all systems, processes, and objects within the universe function in harmony with biological patterns. Living organisms are the result of the universe’s biological pattern and are embedded within their physiology the patterns of this biological universe. Therefore physiological (...) class='Hi'>patterns in living organisms can be used as models to structurally map analogies from the biological domain to any target domain to reveal and understand the biological nature of the target domain. Our paper explores various analogies, structurally mapping a red blood cell to a cup; proteins produced from ribosomes to music produced from instruments; a beating heart to the melting and freezing of Antartica; cells, tissue, organs and blood, to people, organizations, industries, and money, and; bio-economic concepts in cellular society to socioeconomic concepts in human society. It also discusses how phenomena in cellular mitosis can help explain phenomena in the universe, such as black holes, dark matter, dark energy, and the structure of the universe. Building upon the concept of perennial wisdom, our research has provided evidence that the ideas of a biological universe were expressed across many past cultures and historical periods. The implications of this theory are vast, encompassing fields such as physics, science, philosophy, religion, law, economics, politics, and engineering, thus serving as a unifying theory for all knowledge. Our theory is supported by meta-analysis of scientific, historic, and religious literature, observations and first principles logic. (shrink)

Whether man is predisposed to lethal violence, ranging from homicide to warfare, and how that may have impacted human evolution, are among the most controversial topics of debate on human evolution. Although recent studies on the evolution of warfare have been based on various archaeological and ethnographic data, they have reported mixed results: it is unclear whether or notwarfare among prehistoric hunter–gathererswas common enough to be a component of human nature and a selective pressure for the evolution of human behaviour. (...) This paper reports the mortality attributable to violence, and the spatio-temporal pattern of violence thus shown among ancient hunter–gatherers using skeletal evidence in prehistoric Japan (the Jomon period: 13 000 cal BC–800 cal BC). Our results suggest that the mortality due to violence was low and spatio-temporally highly restricted in the Jomon period, which implies that violence including warfare in prehistoric Japan was not common. (shrink)

The article deals with the means of constructing a naturalistic character, the model for which was proposed by French writers: the Goncourt brothers and Émile Zola. Naturalists draw their personage concept from the interpretation of its biological nature. The focus of its depiction is shifted to the study of fundamental features of human nature rather than “variables” of the historical forms of its manifestation. A naturalistic character, being “a biological being” rather than “a set of social relations,” is completely absorbed (...) by the environment. The “social” core of a realistic personage is based on the principles of typification, but the “biological” core of a naturalistic character cannot be a generalized type because in it the individual prevails over the typified. Images of Germinie Lacerteux and Thérèse Raquin from the Goncourts’ and Zola’s same-name novels respectively are considered to be prototypes of naturalistic characters. In Ukrainian literature, Ivan Franko interpreted and synthesized Western European experience using realistic and naturalistic art to create his own concept of “scientific realism.” The difference in Franko’s personage construction lies in the fact that he does not confine himself to the observation and description of his heroes’ behavior but offers a plan for correcting their deficiencies. (shrink)

Aristotle was the first thinker to articulate a taxonomy of scientific knowledge, which he set out in Posterior Analytics. Furthermore, the “special sciences”, i.e., biology, zoology and the natural sciences in general, originated with Aristotle. A classical question is whether the mathematical axiomatic method proposed by Aristotle in the Analytics is independent of the special sciences. If so, Aristotle would have been unable to match the natural sciences with the scientific patterns he established in the Analytics. In this (...) paper, I reject this pessimistic approach towards the scientific value of natural sciences. I believe that there are traces of biology in the Analytics as well as traces of the Analytics’ theory in zoological treatises. Moreover, for a lack of chronological clarity, I think it’s better to unify Aristotle’s model of scientific research, which includes Analytics and the natural sciences together. (shrink)

What does it look like when a group of scientists set out to re-envision an entire field of biology in symbolic and formal terms? I analyze the founding and articulation of Numerical Taxonomy between 1950 and 1970, the period when it set out a radical new approach to classification and founded a tradition of mathematics in systematic biology. I argue that introducing mathematics in a comprehensive way also requires re-organizing the daily work of scientists in the field. Numerical (...) taxonomists sought to establish a mathematical method for classification that was universal to every type of organism, and I argue this intrinsically implicated them in a qualitative re-organization of the work of all systematists. I also discuss how Numerical Taxonomy’s re-organization of practice became entrenched across systematic biology even as opposing schools produced their own competing mathematical methods. In this way, the structure of the work process became more fundamental than the methodological theories that motivated it. (shrink)

The perception of reality by biosystems is based on different, and in certain respects more effective, principles than those utilized by the more formal procedures of science. As a result, what appears as random pattern to the scientific method can be meaningful pattern to a living organism. The existence of this complementary perception of reality makes possible in principle effective use by organisms of the direct interconnections between spatially separated objects shown to exist in the work of J. S. Bell.

This paper aims to provide a philosophical and theoretical account of biological communication grounded in the notion of organisation. The organisational approach characterises living systems as organised in such a way that they are capable to self-produce and self-maintain while in constant interaction with the environment. To apply this theoretical framework to the study of biological communication, we focus on a specific approach, based on the notion of influence, according to which communication takes place when a signal emitted by a (...) sender triggers a change in the behaviour of the receiver that is functional for the sender itself. We critically analyse the current formulations of this account, that interpret what is functional for the sender in terms of evolutionary adaptations. Specifically, the adoption of this etiological functional framework may lead to the exclusion of several phenomena usually studied as instances of communication, and possibly even of entire fields of investigation such as synthetic biology. As an alternative, we reframe the influence approach in organisational terms, characterising functions in terms of contributions to the current organisation of a biological system. We develop a theoretical account of biological communication in which communicative functions are distinguished from other types of biological functions described by the organisational account (e.g. metabolic, ecological, etc.). The resulting organisational-influence approach allows to carry out causal analyses of current instances of phenomena of communication, without the need to provide etiological explanations. In such a way it makes it possible to understand in terms of communication those phenomena which realise interactive patterns typical of signalling interactions – and are usually studied as such in scientific practice – despite not being the result of evolutionary adaptations. Moreover, this approach provides operational tools to design and study communicative interactions in experimental fields such as synthetic biology. (shrink)

Social norms – rules governing which behaviours are deemed appropriate or inappropriate within a given community – are typically taken to be uniquely human. Recently, this position has been challenged by a number of philosophers, cognitive scientists, and ethologists, who have suggested that social norms may also be found in certain non-human animal communities. Such claims have elicited considerable scepticism from norm cognition researchers, who doubt that any non-human animals possess the psychological capacities necessary for normative cognition. However, there is (...) little agreement among these researchers about what these psychological prerequisites are. This makes empirical study of animal social norms difficult, since it is not clear what we are looking for and thus what should count as behavioural evidence for the presence (or absence) of social norms in animals. To break this impasse, we offer an approach that moves beyond contested psychological criteria for social norms. This approach is inspired by the animal culture research program, which has made a similar shift away from heavily psychological definitions of ‘culture’ and to become organized around a cluster of more empirically tractable concepts of culture. Here, we propose an analogous set of constructs built around the core notion of a normative regularity, which we define as a socially maintained pattern of behavioural conformity within a community. We suggest methods for studying potential normative regularities in wild and captive primates. We also discuss the broader scientific and philosophical implications of this research program with respect to questions of human uniqueness, animal welfare and conservation. (shrink)

The scenario of Homo sapiens origin/s within Africa has become increasingly complex, with a pan-African perspective currently challenging the long-established single-origin hypothesis. In this paper, we review the lines of evidence employed in support of each model, highlighting inferential limitations and possible terminological misunderstandings. We argue that the metapopulation scenario envisaged by pan-African proponents well describes a mosaic diversification among late Middle Pleistocene groups. However, this does not rule out a major contribution that emerged from a single population where crucial (...) derived features—notably, a globular braincase—appeared as the result of a punctuated, cladogenetic event. Thus, we suggest that a synthesis is possible and propose a scenario that, in our view, better reconciles with consolidated expectations in evolutionary theory. These indicate cladogenesis in allopatry as an ordinary pattern for the origin of a new species, particularly during phases of marked climatic and environmental instability. (shrink)

In the first part of this article we survey general similarities and differences between biological and social macroevolution. In the second (and main) part, we consider a concrete mathematical model capable of describing important features of both biological and social macroevolution. In mathematical models of historical macrodynamics, a hyperbolic pattern of world population growth arises from non-linear, second-order positive feedback between demographic growth and technological development. Based on diverse paleontological data and an analogy with macrosociological models, we suggest that the (...) hyperbolic character of biodiversity growth can be similarly accounted for by non-linear, second-order positive feedback between diversity growth and the complexity of community structure. We discuss how such positive feedback mechanisms can be modelled mathematically. (shrink)

In the first part of this article we survey general similarities and differences between biological and social macroevolution. In the second (and main) part, we consider a concrete mathematical model capable of describing important features of both biological and social macroevolution. In mathematical models of historical macrodynamics, a hyperbolic pattern of world population growth arises from non-linear, second-order positive feedback between demographic growth and technological development. Based on diverse paleontological data and an analogy with macrosociological models, we suggest that the (...) hyperbolic character of biodiversity growth can be similarly accounted for by non-linear, second-order positive feedback between diversity growth and the complexity of community structure. We discuss how such positive feedback mechanisms can be modelled mathematically. (shrink)

Autoinhibition is a design principle realized in many molecular mechanisms in biology. After explicating the notion of a design principle and showing that autoinhibition is such a principle, we focus on how researchers discovered instances of autoinhibition, using research establishing the autoinhibition of the molecular motors kinesin and dynein as our case study. Research on kinesin and dynein began in the fashion described in accounts of mechanistic explanation but, once the mechanisms had been discovered, researchers discovered that they exhibited (...) a second phenomenon, autoinhibition. The discovery of autoinhibition not only reverses the pattern in terms of which philosophers have understood mechanism discovery but runs counter to the one phenomenon-one mechanism principle assumed to relate mechanisms and the phenomena they explain. The ubiquity of autoinhibition as a design principle, therefore, necessitates a philosophical understanding of mechanisms that recognizes how they can participate in more than one phenomenon. Since mechanisms with this design are released from autoinhibition only when they are acted on by control mechanisms, we advance a revised account of mechanisms that accommodates attribution of multiple phenomena to the same mechanism and distinguishes them from other processes that control them. (shrink)

How the visual systems of different species enable them to detect and discriminate colour patterns and how such visual abilities contribute to their survival is discussed. The influence of evolutionary and environmental pressures on both perceptual capacity and colour trait production is to be considered. Visual systems with different functional anatomy have evolved in response to such pressures.

Among the many causes of an event, how do we distinguish the important ones? Are there ways to distinguish among causes on principled grounds that integrate both practical aims and objective knowledge? Psychologist Tania Lombrozo has suggested that causal explanations “identify factors that are ‘exportable’ in the sense that they are likely to subserve future prediction and intervention” (Lombrozo 2010, 327). Hence portable causes are more important precisely because they provide objective information to prediction and intervention as practical aims. However, (...) I argue that this is only part of the epistemology of causal selection. Recent work on portable causes has implicitly assumed them to be portable within the same causal system at a later time. As a result, it has appeared that the objective content of causal selection includes only facts about the causal structure of that single system. In contrast, I present a case study from systems biology in which scientists are searching for causal factors that are portable across rather than within causal systems. By paying careful attention to how these biologists find portable causes, I show that the objective content of causal selection can extend beyond the immediate systems of interest. In particular, knowledge of the evolutionary history of gene networks is necessary for correctly identifying causal patterns in these networks that explain cellular behavior in a portable way. (shrink)

In the first part of this article we survey general similarities and differences between biological and social macroevolution. In the second (and main) part, we consider a concrete mathematical model capable of describing important features of both biological and social macroevolution. In mathematical models of historical macrodynamics, a hyperbolic pattern of world population growth arises from non-linear, second-order positive feedback between demographic growth and technological development. This is more or less identical with the working of the collective learning mechanism. Based (...) on diverse paleontological data and an analogy with macrosociological models, we suggest that the hyperbolic character of biodiversity growth can be similarly accounted for by non-linear, second-order positive feedback between diversity growth and the complexity of community structure, suggesting the presence within the biosphere of a certain analogue of the collective learning mechanism. We discuss how such positive feedback mechanisms can be modelled mathematically. (shrink)

Climate change continues to have recognizable impacts across the globe, as weather patterns shift and impacts accumulate and intensify. In this wider context, urban areas face significant challenges as they attempt to mitigate dynamic changes at the local level — changes such as those caused by intensifying weather events, the disruption of critical supplies, and the deterioration of local ecosystems. One field that could help urban areas address these challenges is conservation biology. However, this paper presents the argument (...) that work in urban contexts may be especially difficult for conservation biologists. In light of current climate change predictions, conservation biology may need to abandon some of its core values in favor of commitments guiding urban ecology. More broadly, this essay aims to reconcile the goals of restoration and conservation, by reconceptualizing what an ecosystem is, in the context of a world threatened by global climate change. (shrink)

The theory proposing a biological framework for a mathematical universe hypothesis posits that biological patterns define the fundamental nature of reality. These biological patterns are initially hidden from view, but can only be unveiled and understood through the knowledge of biology’s patterns and structurally mapping correspondences from the biological domain to a target domain. This perspective aligns with the ideas establishing perennial wisdom, a concept that encompasses universal and timeless spiritual truths found across various traditions. By (...) exploring the parallels between perennial wisdom's core ideas and the theory of a biological universe, we can assert that the mystical concepts of Pnimiyut and Chitzoniyut from Kabbalah may have been attempting to express the underlying principles surrounding a biological universe. In this essay, we will delve into the concepts of Pnimiyut and Chitzniyut and their potential connection to the biological nature of the universe. (shrink)

Though the realm of biology has long been under the philosophical rule of the mechanistic magisterium, recent years have seen a surprisingly steady rise in the usurping prowess of process ontology. According to its proponents, theoretical advances in the contemporary science of evo-devo have afforded that ontology a particularly powerful claim to the throne: in that increasingly empirically confirmed discipline, emergently autonomous, higher-order entities are the reigning explanantia. If we are to accept the election of evo-devo as our best (...) conceptualisation of the biological realm with metaphysical rigour, must we depose our mechanistic ontology for failing to properly “carve at the joints” of organisms? In this paper, I challenge the legitimacy of that claim: not only can the theoretical benefits offered by a process ontology be had without it, they cannot be sufficiently grounded without the metaphysical underpinning of the very mechanisms which processes purport to replace. The biological realm, I argue, remains one best understood as under the governance of mechanistic principles. (shrink)

Bacteria do many things as organized populations. We have recently learned much about the molecular basis of intercellular communication among prokaryotes. Colonies display bacterial capacities for multicellular coordination which can be useful in nature where bacteria predominantly grow as films, chains, mats and colonies. E. coli colonies are organized into differentiated non-clonal populations and undergo complex morphogenesis. Multicellularity regulates many aspects of bacterial physiology, including DNA rearrangement systems. In some bacterial species, colony development involves swarming (active migration of cell groups). (...) Swarm colony development displays precise geometrical controls and periodic phenomena. Motile E. coli cells in semi-solid media form organized patterns due to chemotactic autoaggregation. On poor media, B. subtilis forms branched colonies using group motility and long-range chemical signalling. The significances of bacterial colony patterns thus reside in a deeper understanding of prokaryotic biology and evolution and in experimental systems for studying self-organization and morphogenesis. (shrink)

A recurring claim in a number of behavioural, cognitive and neuro-scientific literatures is that there is, or must be, a unidimensional ‘common currency’ in which the values of different available options are represented. There is striking variety in the quantities or properties that have been proposed as determinants of the ordering in motivational strength. Among those seriously suggested are pain and pleasure, biological fitness, reward and reinforcement, and utility among economists, who have regimented the notion of utility in a variety (...) of ways, some of them incompatible. This topic deserves philosophical attention for at least the following reasons. Repeated invocation of the ‘common currency’ idiom isn’t merely terminological coincidence because most of the claims are competing explanations either of manifest pattern in choices, or of order in the processes producing choice. We can’t suppose that the different currency claims within each area are compatible, because there are significant obstacles to identifying pairs of members of either the ‘pattern’ or ‘process’ group. There are, finally, seriously opposed positions about the relationships between the pattern facts and the process facts. There are philosophical positions both favouring and opposing a common currency. But direct consideration of the abstract relationships between claims about common currencies across scientific settings, and the arguments for and against these claims, is relatively rare. There is, though, much of philosophical interest to be found here. (shrink)

Evolutionary psychologists often try to “bring together” biology and psychology by making predictions about what specific psychological mechanisms exist from theories about what patterns of behaviour would have been adaptive in the EEA for humans. This paper shows that one of the deepest methodological generalities in evolutionary biology—that proximate explanations and ultimate explanations stand in a many-to-many relation—entails that this inferential strategy is unsound. Ultimate explanations almost never entail the truth of any particular proximate hypothesis. But of (...) course it does not follow that there are no other ways of “bringing together” biology and psychology. Accordingly, this paper explores one other strategy for doing just that, the pursuit of a very specific kind of consilience. However, I argue that inferences reflecting the pursuit of this kind of consilience with the best available theories in contemporary evolutionary biology indicate that psychologists should have a preference for explanations of adaptive behavior in humans that refer to learning and other similarly malleable psychological mechanisms—and not modules or instincts or any other kind of relatively innate and relatively non-malleable psychological mechanism. (shrink)

Imagination is necessary for scientific practice, yet there are no in vivo sociological studies on the ways that imagination is taught, thought of, or evaluated by scientists. This article begins to remedy this by presenting the results of a qualitative study performed on two systems biology laboratories. I found that the more advanced a participant was in their scientific career, the more they valued imagination. Further, positive attitudes toward imagination were primarily due to the perceived role of imagination in (...) problem-solving. But not all problem-solving episodes involved clear appeals to imagination, only maximally specific problems did. This pattern is explained by the presence of an implicit norm governing imagination use in the two labs: only use imagination on maximally specific problems, and only when all other available methods have failed. This norm was confirmed by the participants, and I argue that it has epistemological reasons in its favour. I also found that its strength varies inversely with career stage, such that more advanced scientists do (and should) occasionally bring their imaginations to bear on more general problems. A story about scientific pedagogy explains the trend away from (and back to) imagination over the course of a scientific career. Finally, some positive recommendations are given for a more imagination-friendly scientific pedagogy. (shrink)

In this study, we analyzed the blinking behavior of players in a video game tournament. Our aim was to test whether spontaneous blink patterns differ across levels of expertise. We used blink rate, blink duration, blink frequency, and eyelid movements represented by the Eye Aspect Ratio (EAR) to train a machine learning classifier to discriminate between different levels of expertise. Classifier performance was highly influenced by features such as the mean, standard deviation and median EAR. Moreover, further analysis suggests (...) that blinking rate and blink duration are likely to increase along with the level of expertise. We speculate this may be indicative of a reduction in cognitive load and lowered stress of expert players. In general, our results suggest that EAR and blink patterns can be used to identify different levels of expertise of video game players. (shrink)

The present study collected a larger set of three-dimensional data on human crania from the Kofun period (as well as from previous periods, i.e., the Jomon and Yayoi periods) in the Japanese archipelago (AD 250 to around 700) than previous studies. Three-dimensional geometric morphometrics were employed to investigate human migration patterns in finer-grained phases. These results are consistent with those of previous studies, although some new patterns were discovered. These patterns were interpreted in terms of demic diffusion, (...) archaeological findings, and historical evidence. In particular, the present results suggest the presence of a gradual geological cline throughout the Kofun period, although the middle period did not display such a cline. This discrepancy might reflect social changes in the middle Kofun period, such as the construction of keyhole-shaped mounds in the peripheral regions. The present study implies that a broader investigation with a larger sample of human crania is essential to elucidating macro-level cultural evolutionary processes. (shrink)

Among the factors necessary for the occurrence of some event, which of these are selectively highlighted in its explanation and labeled as causes — and which are explanatorily omitted, or relegated to the status of background conditions? Following J. S. Mill, most have thought that only a pragmatic answer to this question was possible. In this paper I suggest we understand this ‘causal selection problem’ in causal-explanatory terms, and propose that explanatory trade-offs between abstraction and stability can provide a principled (...) solution to it. After sketching that solution, it is applied to a few biological examples, including to a debate concerning the ‘causal democracy’ of organismal development, with an anti-democratic (though not a gene-centric) moral. (shrink)

Debate about cognitive science explanations has been formulated in terms of identifying the proper level(s) of explanation. Views range from reductionist, favoring only neuroscience explanations, to mechanist, favoring the integration of multiple levels, to pluralist, favoring the preservation of even the most general, high-level explanations, such as those provided by embodied or dynamical approaches. In this paper, we challenge this framing. We suggest that these are not different levels of explanation at all but, rather, different styles of explanation that capture (...) different, cross-cutting patterns in cognitive phenomena. Which pattern is explanatory depends on both the cognitive phenomenon under investigation and the research interests occasioning the explanation. This reframing changes how we should answer the basic questions of which cognitive science approaches explain and how these explanations relate to one another. On this view, we should expect different approaches to offer independent explanations in terms of their different focal patterns and the value of those explanations to partly derive from the broad patterns they feature. (shrink)

In the future, human destiny may depend on our ethics. In particular, biotechnology and expansion in space can transform life, raising profound questions. Guidance may be found in Life-centered ethics, as biotic ethics that value the basic patterns of organic gene/protein life, and as panbiotic ethics that always seek to expand life. These life-centered principles can be based on scientific insights into the unique place of life in nature, and the biological unity of all life. Belonging to life then (...) implies a human purpose: to safeguard and propagate life. Expansion in space will advance this purpose but will also raise basic questions. Should we expand all life or only intelligent life? Should we aim to create populations of trillions? Should we seed other solar systems? How far can we change but still preserve the human species, and life itself? The future of all life may be in our hands, and it can depend on our guiding ethics whether life will fulfil its full potentials. Given such profound powers, life-centered ethics can best secure future generations. Our descendants may then understand nature more deeply, and seek to extend life indefinitely. In that future, our human existence can find a cosmic purpose. (shrink)

The central claim of my paper is that pragmatics has a wider scope of application than has been generally appreciated. In particular, I will argue that many discussions of pragmatics are guilty of a problematic form of provincialism. The provincialism at issue restricts the class of target systems of study to those involving groups of developmentally typical humans (or slightly idealized versions thereof), either explicitly as a matter of principle or implicitly as consequence of how it construes the underlying pragmatic (...) notions. In what follows, I will argue that this kind of provincialism is problematic because there are patterns of non-human animal social interaction that cannot be properly explained without recourse to the theoretical tool-kit of pragmatics. Crucially, rejecting provincialism about pragmatics does not entail that there are not important theoretical differences between human and non-human systems of pragmatics. It does, however, require that our core philosophical theories of social interaction and communication be centered on features independent not merely of those at work in human languages but also of uniquely human features of cognition and sociality more generally. (shrink)

We characterize access to empirical objects in biology from a theoretical perspective. Unlike objects in current physical theories, biological objects are the result of a history and their variations continue to generate a history. This property is the starting point of our concept of measurement. We argue that biological measurement is relative to a natural history which is shared by the different objects subjected to the measurement and is more or less constrained by biologists. We call symmetrization the theoretical (...) and often concrete operation which leads to considering biological objects as equivalent in a measurement. Last, we use our notion of measurement to analyze research strategies. Some strategies aim to bring biology closer to the epistemology of physical theories, by studying objects as similar as possible, while others build on biological diversity. (shrink)

How can researchers use race, as they do now, to conduct health-care studies when its very definition is in question? The belief that race is a social construct without “biological authenticity” though widely shared across disciplines in social science is not subscribed to by traditional science. Yet with an interdisciplinary approach, the two horns of the social construct/genetics dilemma of race are not mutually exclusive. We can use traditional science to provide a rigorous framework and use a social-science approach so (...) that “invisible” factors are used to adjust the design of studies on an as-needed basis. One approach is to first observe health-care outcomes and then categorize the outcomes, thus removing genetic differences as racial proxies from the design of the study. From the outcomes, we can then determine if there is a pattern of conceivable racial categories. If needed, we can apply dynamic notions of race to acknowledge bias without prejudice. We can use them constructively to improve outcomes and reduce racial disparities. Another approach is nearly identical but considers race not at all: While analyzing outcomes, we can determine if there are biological differences significant enough to identify classifications of humans. That is, we look for genetic patterns in the outcomes and classify only those patterns. There is no attempt to link those patterns to race. (shrink)

John Wilkins and Malte Ebach respond to the dismissal of classification as something we need not concern ourselves with because it is, as Ernest Rutherford suggested, mere ‘‘stamp collecting.’’ They contend that classification is neither derivative of explanation or of hypothesis-making but is necessarily prior and prerequisite to it. Classification comes first and causal explanations are dependent upon it. As such it is an important (but neglected) area of philosophical study. Wilkins and Ebach reject Norwood Russell Hanson’s thesis that classification (...) relies on observation that is theory-laden and deny the need for aetiological assumptions and historical reconstruction to justify its arrangement. What they offer instead is a significant (albeit controversial) contribution to the philosophical literature on classification, a pre-theoretic natural classification based on the observation of patterns in data of ready-made phenomena. Their notion of ready-made phenomena rests on a conception of tacit knowledge or know-how. This is evident in their distinction between strong Theory-dependence and na ̈ıve theory-dependence. Their small t-theory-dependence permits patterns of observation that facilitate know-how but does not rely on a domain-specific explanatory theory of their aetiology. Wilkins and Ebach suggest classification differs from theory building in that it is passive (whereas theory building is active). Classification is possible just because it does not require the sieve of theory to capture classes that are ‘‘handed to you by your cognitive dispositions and the data that you observe’’ (p. 18). Finding regularities sans-theory is just something we do and can do without any prior theory about the underlying causes or origins of the resultant regularities. Luke Howard’s classification of clouds serves as an exemplar of a passive, theory-free classification system and the periodic table and the DSM help to illustrate this type of non-aetiological patterning. A recurrent theme is the nature of naturalness. For Wilkins and Ebach, the conception of naturalness is not one that is based on the generation or discovery of natural kind categories popular in both the traditional metaphysics of Mill and Wittgenstein as well as updated notions within philosophy of biology such as Boyd’s Homeostatic Property Cluster kinds. Instead, Wilkins and Ebach define the naturalness of classification as the falling into hierarchical patterns, aligning the search for natural arrangement with the aim of systematics, and as something that is grounded in a cognitive task or activity. However, they leave the question of realism v. antirealism open. ‘‘In natural classification...we must have real relations no matter how we might interpret ‘real’’’ (p. 70). There is tension with regard to their ontological commitments as they vacillate between constructive, operationalist, and realist approaches. Wilkins and Ebach initially define real as that which is causal and important (pp. 70–71), and later as that which ‘‘depends in no way upon a mind or observer’’ (p. 122). This makes their claim that there was ‘‘no real theory involved [in the pre-Darwinian classifications of Jussieu and Adanson]’’ (p. 64) difficult to interpret. Cont’d……. (shrink)

Homology is a biological sameness relation that is purported to hold in the face of changes in form, composition, and function. In spite of the centrality and importance of homology, there is no consensus on how we should understand this concept. The two leading views of homology, the genealogical and developmental accounts, have significant shortcomings. We propose a new account, the hierarchical-dependency account of homology, which avoids these shortcomings. Furthermore, our account provides for continuity between special, general, and serial homology.

Essentialism in philosophy is the position that things, especially kinds of things, have essences, or sets of properties, that all members of the kind must have, and the combination of which only members of the kind do, in fact, have. It is usually thought to derive from classical Greek philosophy and in particular from Aristotle’s notion of “what it is to be” something. In biology, it has been claimed that pre-evolutionary views of living kinds, or as they are sometimes (...) called, “natu-ral kinds”, are essentialist. This static view of living things presumes that no tran-sition is possible in time or form between kinds, and that variation is regarded as accidental or inessential noise rather than important information about taxa. In contrast it is held that Darwinian, and post-Darwinian, biology relies upon varia-tion as important and inevitable properties of taxa, and that taxa are not, therefore, kinds but historical individuals. Recent attempts have been made to undercut this account, and to reinstitute essentialism in biological kind terms. Others argue that essentialism has not ever been a historical reality in biology and its predecessors. In this chapter, I shall outline the many meanings of the notion of essentialism in psychology and social science as well as science, and discuss pro- and anti-essentialist views, and some recent historical revisionism. It turns out that nobody was essentialist to speak of in the sense that is antievolutionary in biology, and that much confusion rests on treating the one word, “essence” as meaning a single notion when in fact there are many. I shall also discuss the philosophical implica-tions of essentialism, and what that means one way or the other for evolutionary biology. Teaching about evolution relies upon narratives of change in the ways the living world is conceived by biologists. This is a core narrative issue. (shrink)

We take the potentialities that are studied in the biological sciences (e.g., totipotency) to be an important subtype of biological dispositions. The goal of this paper is twofold: first, we want to provide a detailed understanding of what biological dispositions are. We claim that two features are essential for dispositions in biology: the importance of the manifestation process and the diversity of conditions that need to be satisfied for the disposition to be manifest. Second, we demonstrate that the concept (...) of a disposition (or potentiality) is a very useful tool for the analysis of the explanatory practice in the biological sciences. On the one hand it allows an in-depth analysis of the nature and diversity of the conditions under which biological systems display specific behaviors. On the other hand the concept of a disposition may serve a unificatory role in the philosophy of the natural sciences since it captures not only the explanatory practice of biology, but of all natural sciences. Towards the end we will briefly come back to the notion of a potentiality in biology. (shrink)