Philosophy of Biology, Miscellaneous

This paper aims to develop an account of the pursuitworthiness of models based on a view of models as epistemic tools. This paper is motivated by the historical question of why, in the 1960s, when many scientists hardly found QSAR models attractive, some pharmaceutical scientists pursued Quantitative Structure–Activity Relationship (QSAR) models despite the lack of potential for theoretical development or empirical success. This paper addresses this question by focusing on how models perform their heuristic functions as epistemic tools rather than (...) as potential theories. I argue that models perform their heuristic function by “constructing” phenomena from data in the sense that they allow the model users who interact with the medium of the models to recognise the phenomena as such. The constructed phenomena assist model users in identifying which conditional hypotheses that are focused on low-level regularities concerning entities such as chemical compounds are more “testworthy,” a concept that links the costs associated with hypothesis testing with the fertility of the hypothesis. (shrink)

Recent research about the microbiome points to a picture in which we, humans, are ‘living through’ nature, and nature itself is living in us. Our bodies are hosting—and depend on—the multiple species that constitute human microbiota. This article will discuss current research on the microbiome through the ideas of Japanese ecologist Imanishi Kinji (1902–1992). First, some of Imanishi’s key ideas regarding the world of living beings and multispecies societies are presented. Second, seven types of relationships concerning the human microbiome, human (...) beings, and the environment are explored. Third, inspired by Imanishi’s work, this paper develops the idea of dynamic, porous, and complex multispecies societies in which different living beings or species are codependent on others, including microbiota and human beings. (shrink)

This Open Access book combines philosophical and historical analysis of various forms of alternatives to mechanism and mechanistic explanation, focusing on the 19th century to the present. It addresses vitalism, organicism and responses to materialism and its relevance to current biological science. In doing so, it promotes dialogue and discussion about the historical and philosophical importance of vitalism and other non-mechanistic conceptions of life. It points towards the integration of genomic science into the broader history of biology. It details a (...) broad engagement with a variety of nineteenth, twentieth and twenty-first century vitalisms and conceptions of life. In addition, it discusses important threads in the history of concepts in the United States and Europe, including charting new reception histories in eastern and south-eastern Europe. While vitalism, organicism and similar epistemologies are often the concern of specialists in the history and philosophy of biology and of historians of ideas, the range of the contributions as well as the geographical and temporal scope of the volume allows for it to appeal to the historian of science and the historian of biology generally. (shrink)

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)

Exceptionally preserved fossils are the product of complex interplays of biological and geological processes including burial, autolysis and microbial decay, authigenic mineralization, diagenesis, metamorphism, and finally weathering and exhumation. Determining which tissues are preserved and how biases affect their preservation pathways is important for interpreting fossils in phylogenetic, ecological, and evolutionary frameworks. Although laboratory decay experiments reveal important aspects of fossilization, applying the results directly to the interpretation of exceptionally preserved fossils may overlook the impact of other key processes that (...) remove or preserve morphological information. Investigations of fossils preserving non-biomineralized tissues suggest that certain structures that are decay resistant are rarely preserved, and decay-prone structures can fossilize, albeit rarely. As we review here, decay resistance is an imperfect indicator of fossilization potential, and a suite of biological and geological processes account for the features preserved in exceptional fossils. Organisms decayed experimentally in seawater have been used as direct analogs for soft-bodied fossil taxa, with fossils representing a snapshot of a particular stage of decay. We argue that numerous geological and biological processes account for fossilization and that all of these should be considered when reconstructing extinct organisms. (shrink)

Alan M. Turing’s last published work and some posthumously published manuscripts were dedicated to the development of his theory of organic pattern formation. In “The Chemical Basis of Morphogenesis” (1952), he provided an elaborated mathematical formulation of the theory of the origins of biological form that had been first proposed by Sir D’Arcy Wendworth Thompson in On Growth and Form (1917/1942). While arguably his most mathematically detailed and his systematically most ambitious effort, Turing’s morphogenetical writings also form the most thematically (...) self-contained and least philosophically explored part of his work. We dedicate our inquiry to the reasons and the implications of Turing’s choice of biological topic and viewpoint. We will probe for possible factors in Turing’s choice that go beyond availability and acquaintance with On Growth and Form. On these grounds, we will explore how and to what extent his theory of morphogenesis actually ties in with his concept of mechanistic computation. Notably, Thompson’s pioneering work in biological ‘structuralism’ was organicist in outlook and explicitly critical of the Darwinian approaches that were popular with Turing’s cyberneticist contemporaries—and partly used by Turing himself in his proto-connectionist models of learning. Resolving this apparent dichotomy, we demonstrate how Turing’s quest for mechanistic explanations of how organisation emerges in nature leaves room for a non-mechanist view of nature. (shrink)

In this essay I propose that what design principles in systems biology and systems neuroscience do is to present abstract characterizations of mechanisms, and thereby facilitate mechanistic explanation. To show this, one design principle in systems neuroscience, i.e., the multilayer perceptron, is examined. However, Braillard (2010) contends that design principles provide a sort of non-mechanistic explanation due to two related reasons: they are very general and describe non-causal dependence relationships. In response to this, I argue that, on the one hand, (...) all mechanisms are more or less general (or abstract), and on the other, many (if not all) design principles are causal systems. (shrink)

En los últimos años, algunos autores han venido sosteniendo que la validez de la representación arborescente del patrón filético generado por la evolución está siendo menoscabada por el reconocimiento del impacto evolutivo que tendrían la transferencia genética horizontal, la simbiogénesis, la especiación por hibridación y la introgresión. Esa concepción o representación cladogenética de la evolución sólo nos dejaría ver un aspecto parcial de las relaciones de filiación que conectan a los diferentes linajes de seres vivos; ocultando otro aspecto cuya representación (...) más adecuada sería un reticulado de relaciones entre taxones. Con todo, aún sin poner en tela de juicio la frecuencia y la relevancia explicativa de dichos fenómenos, en este trabajo se intentará mostrar que su admisión y reconocimiento no tiene por qué ir en detrimento de esa concepción cladogenética de la evolución cuya relativización se está pregonando. Por el contrario, la comprensión y la representación de tales fenómenos supone dicha concepción. Palabras clave: Filogénesis, Especiación por hibridación, Introgresión, Simbiogénesis, TGH. (shrink)

Algunos aspectos de La expresión de las emociones de Charles Darwin pueden resultar intrigantes, pues, en la explicación de cómo tales expresiones se originan, Darwin casi nunca apela a la selección natural. En cambio, apela principalmente a la idea de que movimientos voluntarios se asocian a emociones, volviéndose por hábito innatos e involuntarios al heredarse a la descendencia. Si bien Darwin da varias razones para defender esta explicación, en este trabajo trataré de mostrar que, si se entiende el libro sobre (...) las expresiones en relación con los objetivos explícitos e implícitos de El origen del hombre, el asunto se entiende mejor. En particular, resulta interesante la tesis que Desmond y Moore plantean respecto a la importancia de los ideales antiesclavistas de Darwin a la hora del tratamiento de las razas. Defenderé en este trabajo que el enfoque de Desmond y Moore puede extenderse al libro acerca de las expresiones. Específicamente, estableceré vínculos entre la explicación del origen de las razas y la explicación del origen del rubor. Palabras clave: Charles Darwin, La expresión de las emociones, El origen del hombre, Rubor, Antiesclavismo. (shrink)

In both scientific and popular circles it is often said that we are in the midst of a sixth mass extinction. Although the urgency of our present environmental crises is not in doubt, such claims of a present mass extinction are highly controversial scientifically. Our aims are, first, to get to the bottom of this scientific debate by shedding philosophical light on the many conceptual and methodological challenges involved in answering this scientific question, and, second, to offer new philosophical perspectives (...) on what the value of asking this question has been — and whether that value persists today. We show that the conceptual challenges in defining ‘mass extinction’, uncertainties in past and present diversity assessments, and data incommensurabilities undermine a straightforward answer to the question of whether we are in, or entering, a sixth mass extinction today. More broadly we argue that an excessive focus on the mass extinction framing can be misleading for present conservation efforts and may lead us to miss out on the many other valuable insights that Earth’s deep time can offer in guiding our future. (shrink)

Issues surrounding pregnancy loss are rarely addressed in Christian philosophy. Yet a modest estimate based on the empirical and medical literature places the rate of pregnancy loss between fertilization and term at somewhere between 40–60%. If miscarriage really is as common as the research gives us to believe, then it would seem a pressing topic for a Christian philosophy of the future to address. This paper attempts to begin this work by showing how thinking more closely about pregnancy loss understood (...) as a grievable event can have a profound impact on the way we think about particular theoretical debates in Christian philosophy and provide opportunities for the discipline to put its skills to use in the development of helpful conceptual and hermeneutical resources for those grieving such losses. However, this will require seeking out and taking seriously the testimony of those who have undergone pregnancy loss, as well as getting clearer on how best to conceptualize pregnancy and its loss in the first place. (shrink)

ENG: We all have our own ideas about what it is like to be intelligent. Indeed, even the experts disagree on this topic. This has generated diverse theories on the nature of intelligence and its genetic and environmental bases. Many scientific and philosophical questions thus remain unaddressed: is it possible to characterize intelligence in scientific terms? What do IQ tests measure? How is intelligence influenced by genetics, epigenetics, and the environment? What are the ethical and social implications of the research (...) on this topic? This book aims to provide the readers with the conceptual resources to critically analyze scientific findings and orientate themselves in this multi-faceted debate across biology, psychology, neuroscience, philosophy, and anthropology. -/- ITA: Ognuno di noi ha una propria idea di cosa significhi essere intelligenti, tanto che anche gli scienziati esperti in materia hanno opinioni differenti al riguardo. Ciò ha contribuito a generare teorie contrastanti sulla natura dell’intelligenza e su quali siano le sue basi genetiche e ambientali. Non è un caso, dunque, che diverse domande scientifiche e filosofiche restino ancora aperte: è possibile caratterizzare scientificamente l’intelligenza? Cosa misurano i test del QI? In che modo genetica, epigenetica e ambiente influenzano l’intelligenza? Quali sono le implicazioni etiche e sociali della ricerca sull’argomento? Oltre ad analizzare questi problemi, il testo intende fornire gli strumenti concettuali necessari per leggere criticamente i dati scientifici e orientarsi in uno sfaccettato e affascinante dibattito a cavallo tra biologia, psicologia, neuroscienze, filosofia e antropologia. (shrink)

Modern science generally assumes that the same laws of logic apply to mechanical, chemical and biological entities alike because they are all ultimately material objects. This may seem to be so obvious that there would be no need to validate it -- experimentally or logically. In this article we would like to critically examine this assumption and show that from an experiential/observational level, as well as from a rational/logical level, it is not valid. This becomes apparent, for instance, when we (...) consider the simple observation in which we distinguish animate from inanimate objects: those objects that seem to spontaneously move themselves and those that move only when impelled by some applied force outside or beyond the object. This distinction may be valid at the macroscopic level more than at the level of theoretical atomic particles. Thus the detailed nature of spontaneous movement must also be understood. (shrink)

This paper deals with the evolutionary origin and the adaptive function of emotion. I discuss the view that emotions have evolved as functional adaptations in both humans and non-human animals in order to cope with adaptive challenges and to promote fitness. I argue that there is evolutionary continuity between humans and animals in emotions and emotional expressions, and discuss behavioural argument for this thesis, specifically, Darwin’s and Ekman’s research on similarities in how humans and animals express their basic emotions. In (...) addition to this argument, I provide neuroscientific evidence that supports the claim that basic emotions are evolutionary old and shared among humans and many other animals. Finally, I conclude that animal emotions can be considered the bases and roots of our emotions that connect us to other sentient beings. (shrink)

Analytic metaphysics has become increasingly extended into the social domain. The aim of this article is critical self-reflection on the challenges of transferring the tools of analytic metaphysics from classical cases such as the very existence of abstract or composed objects to socially-contested phenomena such as gender and race. In reflecting on the status of metaphysics of race, I formulate a polemical hypothesis of misalignment according to which the tools of analytic metaphysics are not suitable for engaging with complex racial (...) phenomena and politics. In addressing this challenge of misalignment, the article sketches a perspective on critical metaphysics of race as interdisciplinary action research. (shrink)

This paper discusses the evolutionary origin and adaptive functions of emotions, in line with contemporary evolutionary psychology. Drawing upon Charles Darwin’s study of emotional expressions, it is argued that there is an evolutionary continuity among animals in emotional capacities, and that the differences between humans and animals are differences in degree and not in kind. The focus is on basic or primary emotions (joy, fear, sadness, anger), as it has been consistently shown that they are universal and shared among many (...) different species. Basis for this view is the neuroscientific research on brain mechanisms underlying the emotions, especially subcortical brain regions that are proven to be the evolutionary old loci of emotions, homologous across many species. These neuroscientific data provide convincing empirical evidence for the existence of emotional experiences in animals and the evolutionary continuity among species. (shrink)

A Correction to this paper has been published (changed to open access).

A mythopoetic paradigm or perspective sees the world primarily as a dramatic story of competing personal intentions, rather than a system of objective impersonal laws. Asma argued that our contemporary imaginative cognition is evolutionarily conserved-it has structural and functional similarities to premodern Homo sapiens’s cognition. This article will outline the essential features of mythopoetic cognition or adaptive imagination, delineate the adaptive sociocultural advantages of mythopoetic cognition, explain the phylogenetic and ontogenetic mechanisms that give rise to human mythopoetic mind, show how (...) mythopoetic cognition challeng­es contemporary trends in cognitive science and philosophy, and recognize and outline empirical approaches for a new cognitive science of the imagination. (shrink)

Modes of teaching and learning have had to rapidly shift amid the COVID-19 pandemic. As an emergency response, students from Philippine public schools were provided learning modules based on a minimized list of essential learning competencies in Biology. Using a cross-sectional survey method, we investigated students’ perceptions of the Biology self-learning modules (BSLM) that were designed in print and digitized formats according to a constructivist learning approach. Senior high school STEM students from grades 11 (n = 117) and 12 (n (...) = 104) participated in a survey using a 3-point Likert-scale questionnaire uploaded online through Google Forms. The survey results indicate that majority of the students perceived the modules positively, suggesting that aspects of the modules that were salient to students corresponded to essential elements of constructivist pedagogies. However, during interviews, students reported several difficulties in learning with BSLM as it was constrained by, to name a few, the use of unfamiliar words, lack of access to supporting resources, slow internet connection, and time constraints. To address these problems, teachers reported that they gave deadline extensions, complemented modules with other channels of support, and used online and offline platforms for reaching out to students to answer their queries and plan out their schedule for the week. The findings across the data sources point to the complex demands of emergency distance education that teachers, as curriculum designers and enactors, need to bear in mind in order to craft productive pedagogies, constructivist or otherwise, during this unprecedented time. (shrink)

Recently, psychological phenomena have been expanded to new domains, crisscrossing boundaries of organizational levels, with the emergence of areas such as social personality and ecosystem learning. In this contribution, we analyze the ascription of an individual-based concept (personality) to the social level. Although justified boundary crossings can boost new approaches and applications, the indiscriminate misuse of concepts refrains the growth of scientific areas. The concept of social personality is based mainly on the detection of repeated group differences across a population, (...) in a direct transposition of personality concepts from the individual to the social level. We show that this direct transposition is problematic for avowing the nonsensical ascription of personality even to simple electronic devices. To go beyond a metaphoric use of social personality, we apply the organizational approach to a review of social insect communication networks. Our conceptual analysis shows that socially self-organized systems, such as isolated ant trails and bee’s recruitment groups, are too simple to have social personality. The situation is more nuanced when measuring the collective choice between nest sites or foraging patches: some species show positive and negative feedbacks between two or more self-organized social structures so that these co-dependent structures are inter-related by second-order, social information systems, complying with a formal requirement for having social personality: the social closure of constraints. Other requirements include the decoupling between individual and social dynamics, and the self-regulation of collective decision processes. Social personality results to be sometimes a metaphorical transposition of a psychological concept to a social phenomenon. The application of this organizational approach to cases of learning ecosystems, or evolutionary learning, could help to ground theoretically the ascription of psychological properties to levels of analysis beyond the individual, up to meta-populations or ecological communities. (shrink)

Une rétrospective des débats sur l'origine de la vie : le virus ou la cellule ? Le virus a besoin de la cellule pour se répliquer, mais la cellule est une forme plus évoluée à l'échelle évolutive de la vie. Les virus semblent avoir joué un rôle dans des événements tels que l'origine de la vie cellulaire et l'évolution des mammifères. Même la bactérie la plus simple est bien trop complexe pour être apparue spontanément au début de l'évolution. Par la (...) suite, l'évolution a pu produire des systèmes de plus en plus complexes. La première vraie cellule doit déjà avoir été un produit de l'évolution, résultant d'une communauté primordiale. DOI: 10.13140/RG.2.2.27284.53122. (shrink)

This thought piece dealing with the Covid-19 ‘crisis’ was written – in the form of a diary that runs from February to July 2020 – for a special issue of Derrida Today entitled ‘Fire, Flood, Pestilence and Protest’, edited by Nicole Anderson, and published in November 2020. The piece deals with matters of biopolitics, telecommunication, death and mourning through Derrida and Agamben, and interrogates the eventness of what is called an ‘event’.

The study of viruses raises pressing conceptual and philosophical questions about their nature, their classification, and their place in the biological world. A major set of problems concerns the individuality and diachronic identity of a virus: what is the virus, the viral particle (virion) or the entire viral cycle? The correct identification of the virus has significant ontological consequences, also related to the place and time when biological entities begin and end. DOI: 10.13140/RG.2.2.35874.66241.

Ecology is indispensable to understanding the biological world and addressing the environmental problems humanity faces. Its philosophy has never been more important. In this book, James Justus introduces readers to the philosophically rich issues ecology poses. Besides its crucial role in biological science generally, climate change, biodiversity loss, and other looming environmental challenges make ecology's role in understanding such threats and identifying solutions to them all the more critical. When ecology is applied and its insights marshalled to address these problems (...) and guide policy formation, interesting philosophical issues emerge. Justus sets them out in detail, and explores the often ethically charged dimensions of applied ecological science, using accessible language and a wealth of scientifically-informed examples. (shrink)

Some interpreters claim Kant distinguishes between organisms and living things. I argue that this claim is underdetermined by the textual evidence. Once this is recognized, it becomes a real possibility that Kant’s various remarks about the essential properties of living things generalize to organisms as such. This, in turn, generates a puzzle. Kant repeatedly claims that the capacity for representation is essential to the nature of a living thing. If he does not distinguish between living things and organisms, then how (...) might the capacity for representation be essential to the latter? Drawing on the writings of Kant and his contemporaries, I reconstruct a framework within which representational capacities might conceivably be thought to play this role. On this view, what distinguishes an organism from mechanically explicable products of nature is its capacity for endogenous behavior that is instinctual and representationally mediated. (shrink)

Purpose This paper discusses ethical principles that are implicit in second-order cybernetics, with the aim of arriving at a better understanding of how second-order cybernetics frames living in a world with others. It further investigates implications for second-order cybernetics approaches to architectural design, i.e. the activity of designing frameworks for living. -/- Design/methodology/approach The paper investigates the terminology in the second-order cybernetics literature with specific attention to terms that suggest that there are ethical principles at work. It further relates second-order (...) cybernetics to selected notions in phenomenology, pragmatism and transcendental idealism. The comparison allows for conclusions about the specificity of a second-order inquiry. In line with the thematic focus of this journal issue on the framing of shared worlds, the paper further elaborates on questions relating to the activity of designing “worlds” in which people live with others. -/- Findings The paper highlights that a radical openness toward the future and toward the agency of others is inscribed in the conception of second-order cybernetics. It creates a frame of reference for conceiving social systems of all kinds, including environments that are designed to be inhabited. -/- Originality/value The paper identifies an aesthetics grounded in the process of living-with-others as an ethical principle implicit in second-order cybernetics thought. It is an aesthetics that is radically open for the agency of others. Linking aesthetics and ethics, the paper’s contributions will be of specific value for practitioners and theoreticians of design. Considering second-order cybernetics as a practice generally dealing with designing, it also contributes to the wider second-order cybernetics discourse. (shrink)

There is a widespread belief that for their own safety and for the protection of wildlife, cats should be permanently kept indoors. Against this view, I argue that cat guardians have a duty to provide their feline companions with outdoor access. The argument is based on a sophisticated hedonistic account of animal well-being that acknowledges that the performance of species-normal ethological behavior is especially pleasurable. Territorial behavior, which requires outdoor access, is a feline-normal ethological behavior, so when a cat is (...) permanently confined to the indoors, her ability to flourish is impaired. Since cat guardians have a duty not to impair the well-being of their cats, the impairment of cat flourishing via confinement signifies a moral failing. Although some cats assume significant risks and sometimes kill wild animals when roaming outdoors, these important considerations do not imply that all cats should be deprived of the opportunity to access the outdoors. Indeed, they do not, by themselves, imply that any cat should be permanently kept indoors. (shrink)

The language parasite approach refers to the view that language, like a parasite, is an adaptive system that evolves to fit its human hosts. Supported by recent computer simulations, LPA proponents claim that the reason that humans can use languages with ease is not because we have evolved with genetically specified linguistic instincts but because languages have adapted to the preexisting brain structures of humans. This article examines the LPA. It argues that, while the LPA has advantages over its rival, (...) Chomskyan nativism, there are additional factors that may limit linguistic variety that have yet to be identified by its insightful proponents. This article suggests abandoning the search for a decisive cause of language capacity and argues that language evolution is more likely to arise from balancing multiple engineering constraints. (shrink)

本书共分九章内容：第一章论述了生命科学哲学兴起的背景，区分了生命科学哲学研究中的两种理论倾向，指出了生命科学哲学研究的主要问题，最后介绍了国内外生命科学哲学研究的进展；第二章分析了这种解释方式的合理性 及其与因果性解释方式的关系，并由此进一步讨论了生命科学的自主性问题；第三章从不同方面较详细地论述了正反两方面论证的依据，并对各种观点进行了比较，说明生物学理论缺少规律的原因；第四章讨论了还原概念和突现 概念的历史发展，分析了它们各自的认识论和本体论原因，指出了它们各自的优点和局限，最后指出了超越它们的途径；第五章着重讨论了进化论的统计特性与进化过程的决定论和非决定论问题；第六章讨论了生命难以定义的各 种原因，论述了定义生命的两种主要方法；第七章指出了人工生命提出的主要的哲学问题，从不同角度论证了强人工生命的可能性，分析了数字生命的实在论地位，揭示了人工生命所蕴含计算主义世界观；第八章分析了人类基因 组研究的价值及其所可能引起的伦理和法律问题；第九章总结了8年来关于人类克隆的主要争论和观点，并揭示了这些争论给我们的启示。.

The definition of life is a very important issue in the philosophy of biology, but this issue has unfortunately been neglected by the mainstream philosopher of biology for many years. In this paper, the difficulties with and the reasons for defining life are illustrated, the characteristics of life on Earth are explored, ways of defining life are examined, the main definitions of life are explained and evaluated, and finally, a new information definition of life is proposed.

The subject of this edited volume is the idea of levels of organization: roughly, the idea that the natural world is segregated into part-whole relationships of increasing spatiotemporal scale and complexity. The book comprises a collection of essays that raise the idea of levels into its own topic of analysis. Owing to the wide prominence of the idea of levels, the scope of the volume is aimed at theoreticians, philosophers, and practicing researchers of all stripes in the life sciences. The (...) volume’s contributions reflect this diversity, and draw from fields such as developmental biology, evolutionary biology, molecular biology, ecology, cell biology, and neuroscience. The book presents wide-ranging novel insights on causation and levels, the hierarchical structure of evolution, the role of levels in biological theory, and more. (shrink)

This article proposes an abstract mathematical frame for describing some features of cognitive and biological time. We focus here on the so called “extended present” as a result of protentional and retentional activities (memory and anticipation). Memory, as retention, is treated in some physical theories (relaxation phenomena, which will inspire our approach), while protention (or anticipation) seems outside the scope of physics. We then suggest a simple functional representation of biological protention. This allows us to introduce the abstract notion of (...) “biological inertia”. (shrink)

The notion of habit used in neuroscience is an inheritance from a particular theoretical origin, whose main source is William James. Thus, habits have been characterized as rigid, automatic, unconscious, and opposed to goal-directed actions. This analysis leaves unexplained several aspects of human behavior and cognition where habits are of great importance. We intend to demonstrate the utility that another philosophical conception of habit, the Aristotelian, may have for neuroscientific research. We first summarize the current notion of habit in neuroscience, (...) its philosophical inspiration and the problems that arise from it, mostly centered on the sharp distinction between goal-directed actions and habitual behavior. We then introduce the Aristotelian view and we compare it with that of William James. For Aristotle, a habit is an acquired disposition to perform certain types of action. If this disposition involves an enhanced cognitive control of actions, it can be considered a “habit-as-learning”. The current view of habit in neuroscience, which lacks cognitive control and we term “habit-as-routine”, is also covered by the Aristotelian conception. He classifies habits into three categories: (1) theoretical, or the retention of learning understood as “knowing that x is so”; (2) behavioral, through which the agent achieves a rational control of emotion-permeated behavior (“knowing how to behave”); and (3) technical or learned skills (“knowing how to make or to do”). Finally, we propose new areas of research where this “novel” conception of habit could serve as a framework concept, from the cognitive enrichment of actions to the role of habits in pathological conditions. In all, this contribution may shed light on the understanding of habits as an important feature of human action. Habits, viewed as a cognitive enrichment of behavior, are a crucial resource for understanding human learning and behavioral plasticity. (shrink)

A ubiquitous feature of active sleep in mammals and birds is its relative abundance in early development. In rat pups across the first two postnatal weeks, active sleep promotes the expression of synchronized oscillatory activity within and between cortical and subcortical sensorimotor structures. Sensory feedback from self-generated myoclonic twitches – which are produced exclusively during active sleep – also triggers neural oscillations in those structures. We have proposed that one of the functions of active sleep in early infancy is to (...) provide a context for synchronizing developing structures. Specifically, neural oscillations contribute to a variety of neurodevelopmental processes, including synapse formation, neuronal differentiation and migration, apoptosis, and the refinement of topographic maps. In addition, synchronized oscillations promote functional connectivity between distant brain areas. Consequently, any condition or manipulation that restricts active sleep can, in turn, deprive the infant animal of substantial sensory experience, resulting in atypical developmental trajectories. The synchronization of rhythmic neural activity across brain structures provides evidence of communication. In developing sensorimotor networks, such oscillations are triggered most clearly and prominently during REM sleep. We propose that REM sleep provides a context for the emergence and expression of functional connectivity in the developing sensorimotor system. (shrink)

Margulis’ evolutionary theory entails a revision of certain core concepts of traditional biology. One of these changes is related to the hot debate about units of selection. This paper considers Margulis’ proposal as a new research tradition (RT) and evaluates its consequences to the mentioned issue. Three ideas are suggested here: firstly, that her theory represents the revision of many classical biological concepts; secondly, that her position implies a reappraisal of many traditional issues in philosophy of biology; and thirdly, that (...) studying it from Lakatos and Laudan’s ideas about RT allows us to enlighten the richness of her theory. (shrink)

Despite remarkable empirical and methodological advances, our theoretical understanding of the evolutionary processes that made us human remains fragmented and contentious. Here, we make the radical proposition that the cultural communities within which Homo emerged may be understood as a novel exotic form of organism. The argument begins from a deep congruence between robust features of Pan community life cycles and protocell models of the origins of life. We argue that if a cultural tradition, meeting certain requirements, arises in the (...) context of such a “social protocell,” the outcome will be an evolutionary transition in individuality whereby traditions and hominins coalesce into a macroscopic bio-socio-technical system, with an organismal organization that is culturally inherited through irreversible fission events on the community level. We refer to the resulting hypothetical evolutionary individual as a “sociont.” The social protocell provides a preadapted source of alignment of fitness interests that addresses a number of open questions about the origins of shared adaptive cultural organization, and the derived genetic adaptations that support them. Also, social cooperation between hominins is no longer in exclusive focus since cooperation among traditions becomes salient in this model. This provides novel avenues for explanation. We go on to hypothesize that the fate of the hominin in such a setting would be mutualistic coadaptation into a part-whole relation with the sociont, and we propose that the unusual suite of derived features in Homo is consistent with this hypothesis. (shrink)

According to the dual inheritance theory, cultural learning in our species is a biased and highly efficient process of transmitting cultural traits. Here we define a model of cultural learning where social learning is integrated as a complementary element that facilitates the discovery of a specific behavior by an apprentice, and not as a mechanism that works in opposition to individual learning. In that context, we propose that the emergence of the ability to approve or disapprove of offspring behavior, orienting (...) their learning, transformed primate social learning into a cultural transmission system, like that which characterizes our species. Assessor teaching facilitates the replication and/or reconstruction of behaviors that are difficult to imitate and helps to determine which behaviors should be imitated. We also explore the form in which assessor teaching has conditioned the evolution of our abilities to develop cultures in the hominin line, converting us into individuals equipped with what we call a suadens psychology. Our main point is to defend the hypothesis that suadens psychology determines the stability and dynamics that affect the trajectories of many cultural characters. We compare our proposal with other theories about cultural evolution, specifically with dual inheritance theory and cultural attraction theory. (shrink)

With the advent of powerful parallel computers, efforts have commenced to simulate complete mammalian brains. However, so far none of these efforts has produced outcomes close to explaining even the behavioral complexities of animals. In this article, we suggest four challenges that ground this shortcoming. First, we discuss the connection between hypothesis testing and simulations. Typically, efforts to simulate complete mammalian brains lack a clear hypothesis. Second, we treat complications related to a lack of parameter constraints for large-scale simulations. To (...) demonstrate the severity of this issue, we review work on two small-scale neural systems, the crustacean stomatogastric ganglion and the Caenorhabditis elegans nervous system. Both of these small nervous systems are very thoroughly, but not completely understood, mainly due to issues with variable and plastic parameters. Third, we discuss the hierarchical structure of neural systems as a principled obstacle to whole-brain simulations. Different organizational levels imply qualitative differences not only in structure, but in choice and appropriateness of investigative technique and perspective. The challenge of reconciling different levels also undergirds the challenge of simulating and hypothesis testing, as modeling a system is not the same thing as simulating it. Fourth, we point out that animal brains are information processing systems tailored very specifically for the ecological niches the respective animals live in. (shrink)

Graphical AbstractThe culture of chefs from the world's best restaurants is substituted by new trends paradigmatically epitomized by the TV program Masterchef. The authors feel that a similar transformation affects modern research. Recent scientific policies constrict the design of research grants with the aim of short-term maximization of the monetary value generated by the researcher.

Holobionts are symbiotic assemblages composed by a host plus its microbiome. The status of holobionts as individuals has recently been a subject of continuous controversy, which has given rise to two main positions: on the one hand, holobiont advocates argue that holobionts are biological individuals; on the other, holobiont detractors argue that they are just mere chimeras or ecological communities, but not individuals. Both parties in the dispute develop their arguments from the framework of the philosophy of biology, in terms (...) of what it takes for a “conglomerate” to be considered an interesting individual from a biological point of view. However, the debates about holobiont individuality have important ontological implications that have remained vaguely explored from a metaphysical framework. The purpose of this paper is to cover that gap by presenting a metaphysical approach to holobionts individuality. Drawing upon a conception of natural selection that puts the focus on the transgenerational recurrence of the traits and that supports the thesis that holobionts are units of selection, we argue that holobionts bear emergent traits and exert downward powers over the entities that compose them. In this vein, we argue, a reasonable argument can be made for conceiving holobionts as emergent biological individuals. (shrink)