When the history of life on earth is viewed as a history of cell division, all of life becomes a single cell lineage. The growth and differentiation of this lineage in reciprocal interaction with its environment can be viewed as a developmental process; hence the evolution of life on earth can also be seen as the development of life on earth. Here, in reviewing this field, some potentially fruitful research directions suggested by this change in perspective are highlighted. Variation and (...) selection become, for example, bidirectional information flows between scales, while the notions of “cooperation” and “competition” become scale relative. The language of communication, inference, and information processing becomes more useful than the language of causation to describe the interactions of both homogeneous and heterogeneous living systems at any scale. Emerging scale‐free theoretical frameworks such as predictive coding and active inference provide conceptual tools for reconceptualizing biology as the study of a unified, multiscale dynamical system. (shrink)

Meaning has traditionally been regarded as a problem for philosophers and psychologists. Advances in cognitive science since the early 1960s, however, broadened discussions of meaning, or more technically, the semantics of perceptions, representations, and/or actions, into biology and computer science. Here, we review the notion of “meaning” as it applies to living systems, and argue that the question of how living systems create meaning unifies the biological and cognitive sciences across both organizational and temporal scales.

Throughout the biological and biomedical sciences there is a growing need for, prescriptive ‘minimum information’ (MI) checklists specifying the key information to include when reporting experimental results are beginning to find favor with experimentalists, analysts, publishers and funders alike. Such checklists aim to ensure that methods, data, analyses and results are described to a level sufficient to support the unambiguous interpretation, sophisticated search, reanalysis and experimental corroboration and reuse of data sets, facilitating the extraction of maximum value from data (...) sets them. However, such ‘minimum information’ MI checklists are usually developed independently by groups working within representatives of particular biologically- or technologically-delineated domains. Consequently, an overview of the full range of checklists can be difficult to establish without intensive searching, and even tracking thetheir individual evolution of single checklists may be a non-trivial exercise. Checklists are also inevitably partially redundant when measured one against another, and where they overlap is far from straightforward. Furthermore, conflicts in scope and arbitrary decisions on wording and sub-structuring make integration difficult. This presents inhibit their use in combination. Overall, these issues present significant difficulties for the users of checklists, especially those in areas such as systems biology, who routinely combine information from multiple biological domains and technology platforms. To address all of the above, we present MIBBI (Minimum Information for Biological and Biomedical Investigations); a web-based communal resource for such checklists, designed to act as a ‘one-stop shop’ for those exploring the range of extant checklist projects, and to foster collaborative, integrative development and ultimately promote gradual integration of checklists. (shrink)

A proper evaluation of the biological significance of Pavlovian conditioning requires consideration of performance mechanisms. Domjan et al.'s definition of net benefit is simplistic, and their model promotes convergence in behaviour, ignoring the possibility of innovation.

A number of philosophers :171–187, 2011; Arnold 2011, in Ethics Politics XV:101–138, 2013) have argued that agent-based, evolutionary game theory models of the evolution of cooperation fail to provide satisfying explanations of cooperation because they are too disconnected from actual biology. I show how these criticisms can be answered by employing modeling approaches from the situated cognition research program that allow for more biologically detailed models. Using cases drawn from recent situated cognition modeling research, I show how agent-based models of (...) the evolution of cooperation can become more empirically-informed and relevant to explaining the evolution of cooperation in real populations. I argue that because situated cognition models allow for more detailed representations of not just agents’ brains but bodies and environments as well, they can be informed by a much wider breadth of empirical research than traditional agent-based models. Moreover, because the simulated bodies of these agents exhibit particular behaviors, they can be more readily compared to the behaviors of actual organisms. I conclude that employing situated cognition approaches to modeling the evolution of cooperation is a more promising way to investigate the evolution of cooperation than more traditional agent-based evolutionary game theory models. (shrink)

Religious therapeutics is the term I use to designate relations between health and spirituality, and medicine and religion. Dimensions of religious therapeutics include religious meanings that inform medical theory, religious means of healing, health as part of religious life, and religion as a remedy for human suffering. Classical Yoga is analyzed to establish an initial matrix of religious therapeutics with 5 branches: philosophical foundations, soteriology, value theory, physical practice, and cultivation of consciousness. Through comparative criticism of classical Yoga, the study (...) presents a heuristic of religious therapeutics: a model for interpreting relations among healing and liberative functions in world religions. ;Body and health are of instrumental but not ultimate value in classical Yoga: the body is used to transcend itself for attainment of Yoga's soteriological goal, realization of self as pure consciousness. Yoga's Samkhya-based metaphysics contains an unreconciled dualism, and while practice of Yoga is paradigmatic of mind/body holism, Yoga prescribes realization of a spiritual self, independent of material and psychological nature. The study rehabilitates the body in respect of the compatibility of embodiedness with religiousness. ;Other Indian and world traditions suggest dimensions of religious therapeutics both resonant with classical Yoga and lacking from it. India's Ayurvedic medicine represents the sixth branch of religious therapeutics: medical therapeutics. I distill from Ayurvedic and Western sources a set of determinants of health: biological, medical/psychological, cultural, and metaphysical. Significant determinants of health are wholeness, self-identity, and freedom; these are incorporated in discussion of the complementary functions of medicine and religion, grounding the claim that in classical Yoga, liberation is healing in an ultimate sense. ;Tantric yogas utilize material nature for human spiritual progress, and unlike classical Yoga, esteem nature, body/mind, the feminine, and relationality. Tantra provides another branch of religious therapeutics: aesthetic therapeutics. The study anticipates elements of health/medicine in western religions, Buddhism, and Lakota religious philosophy. Sacred speech and song are explored to demonstrate comparative inquiry into religious therapeutics; some Native American Indian and Hindu applications of sacred language are considered. Finally, the model of religious therapeutics is supplemented with community, embracing ecological, social, and religious relationality and communication. (shrink)

Population-based research is enhanced by biological measures, but biological sampling raises complex ethical issues. The third British National Survey of Sexual Attitudes and Lifestyles (Natsal-3) will estimate the population prevalence of five sexually transmitted infections (STIs) (Chlamydia trachomatis, Neisseria gonorrhoeae, human papillomavirus (HPV), HIV and Mycoplasma genitalium) in a probability sample aged 16–44 years. The present work describes the development of an ethical approach to urine testing for STIs, including the process of reaching consensus on whether to return (...) results. The following issues were considered: (1) testing for some STIs that are treatable and for which appropriate settings to obtain free testing and advice are widely available (Natsal-3 provides all respondents with STI and healthcare access information), (2) limits on test accuracy and timeliness imposed by survey conditions and sample type, (3) testing for some STIs with unknown clinical and public health implications, (4) how a uniform approach is easier to explain and understand, (5) practical difficulties in returning results and cost efficiency, such as enabling wider STI testing by not returning results. The agreed approach, to perform voluntary anonymous testing with specific consent for five STIs without returning results, was approved by stakeholders and a research ethics committee. Overall, this was acceptable to respondents in developmental piloting; 61% (68 of 111) of respondents agreed to provide a sample. The experiences reported here may inform the ethical decision making of researchers, research ethics committees and funders considering population-based biological sampling. (shrink)

Heart disease is the leading cause of death amongst adult Americans and has recently become a top killer worldwide. The direct costs of cardiovascular disease are projected to triple in the next 20 years, from $272.5 billion to $818.1 billion (Heidenreich et al. 2011). Although there has been a decreased incidence and prevalence of ischemic heart disease over the past several decades in the United States, heart failure remains a major cause of morbidity and mortality. In the United States, approximately (...) 500,000 to 700,000 new cases are identified each year (Lloyd-Jones et al. 2009). Heart failure is now the number one diagnosis leading to hospitalization. As such, it is an increasingly heavy economic burden on .. (shrink)

Culture can be said to be about the business of 'self-replication'. From the moment of conception, it impresses its patterns and rhythms on the developing, infinitely plastic neuronal substrate of the fetal organism. It shapes this substrate to become preferentially sensitive to its patterns and thus to seek to replicate them as an adult. This process of neural shaping continues throughout life as the capacity of the brain to reorganize itself according to the uses to which it addresses itself never (...) ceases. The extraordinary capacity of culture to extract different abilities from the biological form is clearly manifest in the lexical, vocal, tool manufacture, and writing capabilities emerging in bonobos raised in a Pan/Homo culture. These findings render moot old questions regarding the innate limits of the ape brain. They raise instead far more productive questions about the form and function of the perpetual dance that is constantly taking place between plastic neuronal systems and their external culturally devised ways of being. (shrink)

The development of the Functional Genomics Investigation Ontology (FuGO) is a collaborative, international effort that will provide a resource for annotating functional genomics investigations, including the study design, protocols and instrumentation used, the data generated and the types of analysis performed on the data. FuGO will contain both terms that are universal to all functional genomics investigations and those that are domain specific. In this way, the ontology will serve as the “semantic glue” to provide a common understanding of data (...) from across these disparate data sources. In addition, FuGO will reference out to existing mature ontologies to avoid the need to duplicate these resources, and will do so in such a way as to enable their ease of use in annotation. This project is in the early stages of development; the paper will describe efforts to initiate the project, the scope and organization of the project, the work accomplished to date, and the challenges encountered, as well as future plans. (shrink)

The transition from primary to secondary education is one of the most stressful events in a young person’s life (Zeedyk et al., 2003) and can have a negative impact on psychological wellbeing and academic achievement. One explanation for these negative impacts is that the transition coincides with early adolescence, a period during which certain psychological disorders (i.e., anxiety disorders) become more salient (Kessler et al., 2005) and marked social, biological, and psychological development occurs (Anderson, Jacobs, Schramm, & Splittgerber, 2000). (...) This review evaluates the existing literature on the psychological and academic impacts of the transition to secondary education on young adolescents. We examine the factors that plausibly increase or mitigate the risk of developing mental health issues and/or a decline in academic performance during the transition to secondary education. We also review the interplay between psychological health and academic achievement across and beyond the transition. We conclude with a summary of what schools and parents can learn from these findings to support children in a successful transition into secondary education. (shrink)

This article presents an update on known and unknown biological codes. While the genetic code has been recognized as a code for decades, most other codes were hidden in the shadow of this hallmark discovery. It was the dawn of the new millennium when the histone language and code were proclaimed in the years 2000 and 2001, respectively, marking the start of an explosion in the number of published codes across all biological disciplines since then. Actually, there are (...) hundreds to thousands of biological codes, but only a fraction—although still a substantial number—have been explicitly described as such. A first assessment of those codes allows for a simple categorization into structural and regulatory codes, at the same time maintaining Marcello Barbieri´s initial differentiation of organic versus neural codes. The article reviews prominent codes and showcases restriction-modification and toxin-antitoxin systems as code systems that have gone unrecognized until today. This article should read as a motivation for all those who want to discover ever more new codes—from literature or in the field. (shrink)

Biological field stations proliferated in the Rocky Mountains region of the western United States during the early decades of the twentieth century. This essay examines these Rocky Mountain field stations as hybrid lab-field sites from the perspective of the field side of the dichotomy: as field sites with raised walls rather than as laboratories whose walls with the natural world have been lowered. Not only were these field stations transformed to be more like laboratories, but they were also embedded (...) within the particular regional environmental and institutional context of the Rocky Mountains. Using the University of Colorado’s Mountain Laboratory at Tolland and other contemporaneous sites as examples, this essay analyzes key features of these sites, including their location within transportation networks, buildings, equipment, personnel, scheduling, recreational and social activities, and other material and social practices on the ground. Considering both the distinctive and shared characteristics of the Rocky Mountain field stations in comparison to other types of field stations provides a more complete picture of the diversity and range of lab-field hybrid sites in the biological sciences in the early twentieth-century United States. (shrink)

Este artículo tiene por objetivo general indagar acerca de los procesos de institucionalización de una nueva disciplina científica. En particular, se analizan los desplazamientos que se producen entre disciplinas al emerger una nueva: la biología molecular. Se presenta en este artículo el caso del Instituto Nacional de Tecnología Agropecuaria (INTA) de Argentina, institución creada en 1956 para realizar investigaciones, innovaciones y extensionismo para el sector agropecuario. De esa manera, el trabajo presenta los cambios en las disciplinas de las que provienen (...) los investigadores del INTA, desde su creación en 1956 hasta 2010. La investigación que se presenta se centra en un análisis cuantitativo en relación a las disciplinas de origen de los investigadores que se incorporaron a la institución. Al mostrar los desplazamientos entre disciplinas, este artículo pretende contribuir al estudio sobre los conflictos entre las mismas. Pues se sugiere que la emergencia de una nueva disciplina no implica solamente la apertura de nuevas profesiones, instituciones, temas y técnicas de investigación, sino también el desplazamiento de otras anteriormente instaladas, y que tales desplazamientos estarían en la raíz de las tensiones que se registran en la institucionalización de una nueva disciplina. This article aims to investigate the process of institutionalization of a new scientific discipline. In particular, the displacements that occur between disciplines with the emergence of a new one: molecular biology. The case presented in this article is the National Institute of Agricultural Technology (INTA) of Argentina, institution created in 1956 for research, innovation and extension to the agricultural sector. Thus, the paper presents the changes in the disciplines from which INTA's researchers come, since its inception in 1956 until 2010. The research presented in this article focuses on a quantitative analysis in relation to the disciplines of origin of the researchers who joined the institution. By showing the displacements between disciplines, this article aims to contribute to the study of the conflicts between them. For it suggests that the emergence of a new discipline involves not only the opening of new professions, institutions, research subjects and techniques, but also the displacement of other previously installed. These displacements would be at the root of the tensions that occur in the institutionalization of a new discipline. (shrink)

I use a recent ‘experimental philosophy’ study of the concept of the gene conducted by myself and collaborators to discuss the broader epistemological framework within which that research was conducted, and to reflect on the relationship between science, history and philosophy of science, and society.Keywords: Experimental philosophy; Biohumanities; Representing Genes Project; Gene concept; Science criticism; Conceptual ecology.

This paper presents two interpretations of the fiber bundle fonnalism that is applicable to all gauge field theories. The constructionist interpretation yields a substantival spacetime. The analytic interpretation yields a structural spacetime, a third option besides the familiar substantivalism and relationalism. That the same mathematical fonnalism can be derived in two different ways leading to two different ontological interpretations reveals the inadequacy of pure fonnal arguments.

The Reeh-Schlieder theorem asserts the vacuum and certain other states to be spacelike superentangled relative to local quantum fields. This motivates an inquiry into the physical status of various concepts of localization. It is argued that a covariant generalization of Newton-Wigner localization is a physically illuminating concept. When analyzed in terms of nonlocally covariant quantum fields, creating and annihilating quanta in Newton-Wigner localized states, the vacuum is seen to not possess the spacelike superentanglement that the Reeh-Schlieder theorem displays (...) relative to local fields, and to be locally empty as well as globally empty. Newton-Wigner localization is then shown to be physically interpretable in terms of a covariant generalization of the center of energy, the two localizations being identical if the system has no internal angular momentum. Finally, some of the counterintuitive features of Newton-Wigner localization are shown to have close analogues in classical special relativity. (shrink)

We analyze the “Logical fallacies and reasonable debates in invasion biology: a response to Guiaşu and Tindale” article by Frank et al., and also discuss this work in the context of recent intense debates in invasion biology, and reactions by leading invasion biologists to critics of aspects of their field. While we acknowledge the attempt by Frank et al., at least in the second half of their paper, to take into account more diverse points of view about non-native species and (...) their complex roles in ecosystems, we also find the accusations of misrepresenting invasion biology, for instance by “cherry-picking” and “constructing ‘straw people’”, directed at the Guiaşu and Tindale study to be unwarranted. Despite the sometimes harsh responses by leading invasion biologists to critics of their field, we believe that persistent and fundamental problems remain in invasion biology, and we discuss some of these problems in this article. Failing to recognize these problems, and simply dismissing or minimizing legitimate criticisms, will not advance the cause, or enhance the general appeal, of invasion biology and will prevent meaningful progress in understanding the multiple contributions non-native species can bring to various ecosystems worldwide. We recommend taking a more open-minded and pragmatic approach towards non-native species and the novel ecosystems they are an integral part of. (shrink)

We analyzed stable patients’ views regarding synthetic biology in general, the medical application of synthetic biology, and their potential participation in trials of synthetic biology in particular. The aim of the study was to find out whether patients’ views and preferences change after receiving more detailed information about synthetic biology and its clinical applications. The qualitative study was carried out with a purposive sample of 36 stable patients, who suffered from diabetes or gout. Interviews were transcribed verbatim, translated and fully (...) anonymized. Thematic analysis was applied in order to examine stable patients’ attitudes towards synthetic biology, its medical application, and their participation in trials. When patients were asked about synthetic biology in general, most of them were anxious that something uncontrollable could be created. After a concrete example of possible future treatment options, patients started to see synthetic biology in a more positive way. Our study constitutes an important first empirical insight into stable patients’ views on synthetic biology and into the kind of fears triggered by the term “synthetic biology.” Our results show that clear and concrete information can change patients’ initial negative feelings towards synthetic biology. Information should thus be transmitted with great accuracy and transparency in order to reduce irrational fears of patients and to minimize the risk that researchers present facts too positively for the purposes of persuading patients to participate in clinical trials. Potential participants need to be adequately informed in order to be able to autonomously decide whether to participate in human subject research involving synthetic biology. (shrink)

The concept of causality as it appears in a specific scientific theory involves two factors: the relation of necessary connection between the states of a system at different times, and the definition of state at a given time.

The genetic code appeared on Earth at the origin of life, and the codes of culture arrived almost four billion years later. For a long time it has been assumed that these are the only codes that exist in Nature, and if that were true we would have to conclude that codes are extraordinary exceptions that appeared only at the beginning and at the end of the history of life. In reality, various other organic codes have been discovered in the (...) past few decades and it is likely that more will come to light in the future. The existence of many organic codes in Nature is therefore an experimental fact, but also more than that. It is one of those facts that have extraordinary implications. In this book it is shown that the genetic code was a precondition for the origin of the first cells, the signal transduction codes divided the first cells into three primary kingdoms (Archaea, Bacteria and Eukarya), the splicing codes were instrumental to the origin of the eukaryotic nucleus, the histone code provided a new regulation system in eukaryotic genomes, and the cytoskeleton codes allowed the Eukarya to perform internal movements, including those of mitosis and meiosis. It is shown, furthermore, that organic codes had a key role in multicellular life, in particular in the origin of animals, the origin of mind and the origin of language. The great events of macroevolution, in other words, were associated with the appearance of new organic codes, and we can easily understand why. The reason is that a new code brings into existence something that has never existed before because it creates arbitrary associations, relationships that are not determined by physical necessity. Another outstanding implication is the fact that codes involve meaning and we need therefore to introduce in biology, with the standard methods of science, not only the concept of biological information but also that of biological meaning. The research on biological codes, in conclusion, is bringing to light new mechanisms in evolution and new fundamental concepts in science. This research is the field of Code Biology, the study of all codes of life, from the genetic code to the codes of culture, from the origin of life to the origin of man. (shrink)

Systems Biology and the Modern Synthesis are recent versions of two classical biological paradigms that are known as structuralism and functionalism, or internalism and externalism. According to functionalism (or externalism), living matter is a fundamentally passive entity that owes its organization to external forces (functions that shape organs) or to an external organizing agent (natural selection). Structuralism (or internalism), is the view that living matter is an intrinsically active entity that is capable of organizing itself from within, with purely (...) internal processes that are based on mathematical principles and physical laws. At the molecular level, the basic mechanism of the Modern Synthesis is molecular copying, the process that leads in the short run to heredity and in the long run to natural selection. The basic mechanism of Systems Biology, instead, is self-assembly, the process by which many supramolecular structures are formed by the spontaneous aggregation of their components. In addition to molecular copying and self-assembly, however, molecular biology has uncovered also a third great mechanism at the heart of life. The existence of the genetic code and of many other organic codes in Nature tells us that molecular coding is a biological reality and we need therefore a framework that accounts for it. This framework is Code biology, the study of the codes of life, a new field of research that brings to light an entirely new dimension of the living world and gives us a completely new understanding of the origin and the evolution of life. (shrink)

The past decade has been marked by a series of global crises, presenting an opportunity to reevaluate the relationship between science and politics. The biological sciences are instrumental in understanding natural phenomena and informing policy decisions. However, scholars argue that current scientific expertise often fails to account for entire populations and long-term impacts, hindering efforts to address issues such as biodiversity loss, global warming, and pandemics. This article explores the structural challenges of integrating an evolutionary perspective, historically opposed to (...) functional determinants of health and disease, into current biological science practices. Using data on Swiss biology professors from 1957, 1980, and 2000, we examine the structural power dynamics that have led to the division between these competing epistemologies, and how this division has influenced resource allocation and career trajectories. Our analysis suggests that this cleavage presents a significant obstacle to achieving fruitful reconciliations, and that increased academicization and internationalization may benefit functional biologists at the expense of evolutionary biologists. While evolutionary biologists have gained symbolic recognition in recent years, this has not translated into valuable expertise in the political domain. (shrink)

The aim of this book is to show how supramolecular complexity of cell organization can dramatically alter the functions of individual macromolecules within a cell. The emergence of new functions which appear as a consequence of supramolecular complexity, is explained in terms of physical chemistry. The book is interdisciplinary, at the border between cell biochemistry, physics and physical chemistry. This interdisciplinarity does not result in the use of physical techniques but from the use of physical concepts to study biological (...) problems. In the domain of complexity studies, most works are purely theoretical or based on computer simulation. The present book is partly theoretical, partly experimental and theory is always based on experimental results. Moreover, the book encompasses in a unified manner the dynamic aspects of many different biological fields ranging from dynamics to pattern emergence in a young embryo. The volume puts emphasis on dynamic physical studies of biological events. It also develops, in a unified perspective, this new interdisciplinary approach of various important problems of cell biology and chemistry, ranging from enzyme dynamics to pattern formation during embryo development, thus paving the way to what may become a central issue of future biology. (shrink)

I discuss two uses of the concept of the morphogenetic field, a tool of the 19th century biology motivated by particular ontological views of the time, which has been re-emerging and increasingly relevant in explaining microbiological phenomena. I also consider the relation of these uses to the Central Dogma of modern biology as well as Modern Synthesis of Darwinism and genetics. An induced morphogenetic field is determined by a physical field, or it acquires a physical field?s characteristics. Such a morphogenetic (...) field presents only a weak challenge to the Central Dogma of Modern Synthesis by indirectly, albeit severely, constraining variability at the molecular level. I discuss explanations that introduce structural inheritance in ciliate protozoa, as well as the experimental evidence on which these arguments are based. The global cellular morphogenetic field is a unit of such inheritance. I discuss relevant cases of structural inheritance in ciliates that bring about internal cellular as well as functional changes and point out that DNA is absent in the cortex and that RNA controls neither intermediary nor the global level of the field. I go on to argue that utilizing knowledge of known physical fields may advance explanations and understanding of the morphogenetic field in ciliates as the unit of both development and inheritance. (shrink)

An adequate account of how inferences and discoveries are made in modern biology is a difficult prospect for a philosopher. Do we really deduce conclusions from Darwin’s principles? Once Darwinian biology is integrated with molecular biology, can we deduce the organism from its DNA? What does induction look like in an era where data sets are often too large to be processed by a human being? What is the role of abductive explanatory claims that try to define the biological (...) individual in relation to the microbiome with which it may be associated, or to revise the notion of evolution when the interaction of organism and environment comes to seem much more complex than earlier generations imagined. How should we evaluate “origins of life” experiments conducted in the laboratory, where chemistry shifts to biology and we try to recreate early conditions on earth to which we have no empirical access? How are the carefully controlled conditions in the lab to be brought into productive relationship with the messy, contingent outdoor work of biologists in the field, studying crabs or eelgrass at the edge of the Pacific Ocean, or prairie plants at the end of woods, on the plains of the Midwest. To answer these questions, I sent my graduate student Tano Posteraro to work with Ted Grosholz, a marine biologist at the University of California / Davis, and my undergraduate student Alex Grigas to work with Ruth Geyer Shaw, a population geneticist at the University of Minnesota. They came back with complex and interesting answers to these questions. (shrink)

What makes a biological entity an individual? Jack Wilson shows that past philosophers have failed to explicate the conditions an entity must satisfy to be a living individual. He explores the reason for this failure and explains why we should limit ourselves to examples involving real organisms rather than thought experiments. This book explores and resolves paradoxes that arise when one applies past notions of individuality to biological examples beyond the conventional range and presents an analysis of identity (...) and persistence. The book's main purpose is to bring together two lines of research, theoretical biology and metaphysics, which have dealt with the same subject in isolation from one another. Wilson explains an alternative theory about biological individuality which solves problems which cannot be addressed by either field alone. He presents a more fine-grained vocabulary of individuation based on diverse kinds of living things, allowing him to clarify previously muddled disputes about individuality in biology. (shrink)

Annotation. "What is life? What does it means to be alive? Is the Earth a super-organism? Is God necessary? In Biology and the Riddle of Life Charles Birch confronts these fundamental questions at a time when such topics as genetic engineering, cloning and ecology have been prominent in the news. Birch confronts the impression that modern biology has answers to all that there is to be known about life. We need to move towards an understanding of living creatures as subjects, (...) and not only as objects, in order to probe life's hidden secrets - what it is to be alive, what it is to experience pain, and what it is to be in love. The answer must include the meaning of life for us as individuals. Birch proposes a new perspective to bring subject and object together. This is the black box he has opened."--BOOK JACKET. Title Summary field provided by Blackwell North America, Inc. All Rights Reserved. (shrink)

Providing a new conceptual scaffold for further research in biology and cognition, this book introduces the new field of cognitive biology, a systems biology approach showing that further progress in this field will depend on a deep recognition of developmental processes, as well as on the consideration of the developed organism as an agent able to modify and control its surrounding environment. The role of cognition, the means through which the organism is able to cope with its environment, cannot be (...) underestimated. In particular, it is shown that this activity is grounded on a theory of information based on Bayesian probabilities. The organism is considered as a cybernetic system able to integrate a processor as a source of variety (the genetic system), a regulator of its own homeostasis (the metabolic system), and a selecting system separating the self from the non-self (the membrane in unicellular organisms). Any organism is a complex system that can survive only if it is able to maintain its internal order against the spontaneous tendency towards disruption. Therefore, it is forced to monitor and control its environment and so to establish feedback circuits resulting in co-adaptation. Cognitive and biological processes are shown to be inseparable. (shrink)

In many fields of biology, researchers explain a phenomenon by characterizing the responsible mechanism. This requires identifying the candidate mechanism, decomposing it into its parts and operations, recomposing it so as to understand how it is organized and its operations orchestrated to generate the phenomenon, and situating it in its environment. Mechanistic researchers have developed sophisticated tools for decomposing mechanisms but new approaches, including modeling, are increasingly being invoked to recompose mechanisms when they involve nonsequential organization of nonlinear operations. (...) The results often are dynamical mechanistic explanations. The steps in mechanistic research are illustrated using research on circadian rhythms. (shrink)

In discussing the origins of the antievolution movement in American high schools within the framework of science and religion, much is overlooked about the influence of educational trends in shaping this phenomenon. This was especially true in the years before the 1925 Scopes trial, the beginnings of the school antievolution movement. There was no sudden realization in the 1920's – sixty years after the "Origin of Species" was published – that Darwinism conflicted with the Bible, but until evolution was being (...) taught in the high schools, there was no impetus to outlaw it. The creation of "civic biology" curricula in the late 1910's and early 20's, spearheaded by a close-knit community of textbook authors, brought evolution into the high school classroom as part of a complete reshaping of "biology" as a school subject. It also incorporated progressive ideologies about the purposes of compulsory public education in shaping society, and civic biology was fundamentally focused on the applications of the life sciences to human life. Antievolution legislation was part of a broader response to the ideologies of the new biology field, and was a reaction not only to the content of the new subject, but to the increasingly centralized control and regulation of education. Viewing the early school antievolution movement through the science-religion conflict is an artifact of the Scopes trial's re-creation of its origins. What largely caused support for the school antievolution movement in the South and particularly Tennessee were concerns over public education, which biology came to epitomize. (shrink)

Many scientific models in biology are how-possibly models. These models depict things as they could be, but do not necessarily capture actual states of affairs in the biological world. In contemporary philosophy of science, it is customary to treat how-possibly models as second-rate theoretical tools. Although possibly important in the early stages of theorizing, they do not constitute the main aim of modelling, namely, to discover the actual mechanism responsible for the phenomenon under study. In the paper it is (...) argued that this prevailing picture does not do justice to the synthetic strategy that is commonly used in biological engineering. In synthetic biology, how-possibly models are not simply speculations or eliminable scaffolds towards a single how-actually model, but indispensable design hypotheses for a field whose ultimate goal is to build novel biological systems. The paper explicates this by providing an example from the study of alternative genetic systems by synthetic biologist Steven Benner and his group. The case will also highlight how the method of synthesis, even when it fails, provides an effective way to limit the space of possible models for biological systems. (shrink)

In recent years, an increasing number of medical books and papers attempting to analyse the concepts of health and disease from the perspective of evolutionary biology have been published.This paper introduces the evolutionary approach to health and disease in an attempt to illuminate the premisses and the framework of Darwinian medicine. My primary aim is to analyse to what extent evolutionary theory provides for a biological definition of the concept of disease. This analysis reveals some important differences between functional (...) explanations in the field of evolutionary biology and functional explanations in the field of medicine. Moreover, I shall argue that the biological functions relevant to the health of an organism cannot be determined on the basis of evolutionary theory. Accordingly, it seems that Darwinian medicine does not provide for the definition of a biological concept of disease. Still,Darwinian medicine may suggest why we are susceptible to certain diseases; it might also prove a suggestive heuristic on the basis of which new hypotheses concerning relevant treatments of various diseases might be advanced. (shrink)