This paper argues in defense of theanti-reductionist consensus in the philosophy ofbiology. More specifically, it takes issues with AlexRosenberg's recent challenge of this position. Weargue that the results of modern developmentalgenetics rather than eliminating the need forfunctional kinds in explanations of developmentactually reinforce their importance.

The aim of this dissertation is to provide an analysis of central concepts in philosophy of science from the perspective of current molecular and developmental research. Each chapter explores the ways in which particular phenomena or discoveries in molecular biology influences our philosophical understanding of the nature of scientific knowledge. The introductory prologue draws some general connections between the various threads, which revolve around two central themes: causation and explanation. Chapter Two identifies a particular type of (...) causal relation which is widespread across the sciences, but cannot be straightforwardly accommodated by extant accounts of causation and causal explanation. Chapter Three explores how the form of redundant causality identified in the previous chapter plays an important role in causal explanation, by making the effect stable and robust. Chapter Four offers a novel perspective on the debate over biological reductionism by distinguishing between different paradigms of molecular explanation. Chapter Five provides a philosophical analysis of the so-called "Developmental Synthesis" of evolutionary and developmental biology, and suggests a general account of scientific unification grounded in the notion of explanatory relevance. Chapter Six offers an account of dispositional properties inspired by mechanisms of gene regulation, according to which dispositions are not properties of entities, but properties that describe the behavior of abstract idealized models. Finally, Chapter Seven scrutinizes the concept of the molecular ecosystem, a metaphor frequently employed by biologists to describe cellular interactions, but seldom articulated in detail. (shrink)

Philosophical discussion of molecular and developmental biology began in the late 1960s with the use of genetics as a test case for models of theory reduction. With this exception, the theory of natural selection remained the main focus of philosophy of biology until the late 1970s. It was controversies in evolutionary theory over punctuated equilibrium and adaptationism that first led philosophers to examine the concept of developmental constraint. Developmental biology also gained in prominence (...) in the 1980s as part of a broader interest in the new sciences of self-organization and complexity. The current literature in the philosophy of molecular and developmental biology has grown out of these earlier discussions under the influence of twenty years of rapid and exciting growth of empirical knowledge. Philosophers have examined the concepts of genetic information and genetic program, competing definitions of the gene itself and competing accounts of the role of the gene as a developmental cause. The debate over the relationship between development and evolution has been enriched by theories and results from the new field of 'evolutionary developmental biology'. Future developments seem likely to include an exchange of ideas with the philosophy of psychology, where debates over the concept of innateness have created an interest in genetics and development. (shrink)

Significant progress in the molecular investigation of endogenous bioelectric signals during pattern formation in growing tissues has been enabled by recently developed techniques. Ion flows and voltage gradients produced by ion channels and pumps are key regulators of cell proliferation, migration, and differentiation. Now, instructive roles for bioelectrical gradients in embryogenesis, regeneration, and neoplasm are being revealed through the use of fluorescent voltage reporters and functional experiments using well‐characterized channel mutants. Transmembrane voltage gradients (Vmem) determine anatomical polarity and function (...) as master regulators during appendage regeneration and embryonic left‐right patterning. A state‐of‐the‐art recent study reveals that they can also serve as prepatterns for gene expression domains during craniofacial patterning. Continued development of novel tools and better ways to think about physical controls of cell‐cell interactions will lead to mastery of the morphogenetic information stored in physiological networks. This will enable fundamental advances in basic understanding of growth and form, as well as transformative biomedical applications in regenerative medicine. (shrink)

The theory of concepts advanced in the dissertation aims at accounting for a) how a concept makes successful practice possible, and b) how a scientific concept can be subject to rational change in the course of history. Traditional accounts in the philosophy of science have usually studied concepts in terms only of their reference; their concern is to establish a stability of reference in order to address the incommensurability problem. My discussion, in contrast, suggests that each scientific concept consists of (...) three components of content: 1) reference, 2) inferential role, and 3) the epistemic goal pursued with the concept's use. I argue that in the course of history a concept can change in any of these three components, and that change in one component—including change of reference—can be accounted for as being rational relative to other components, in particular a concept's epistemic goal.This semantic framework is applied to two cases from the history of biology: the homology concept as used in 19th and 20th century biology, and the gene concept as used in different parts of the 20th century. The homology case study argues that the advent of Darwinian evolutionary theory, despite introducing a new definition of homology, did not bring about a new homology concept (distinct from the pre-Darwinian concept) in the 19th century. Nowadays, however, distinct homology concepts are used in systematics/evolutionary biology, in evolutionary developmental biology, and in molecular biology. The emergence of these different homology concepts is explained as occurring in a rational fashion. The gene case study argues that conceptual progress occurred with the transition from the classical to the molecular gene concept, despite a change in reference. In the last two decades, change occurred internal to the molecular gene concept, so that nowadays this concept's usage and reference varies from context to context. I argue that this situation emerged rationally and that the current variation in usage and reference is conducive to biological practice.The dissertation uses ideas and methodological tools from the philosophy of mind and language, the philosophy of science, the history of science, and the psychology of concepts. (shrink)

The history of developmental biology is interwoven with debates as to whether mechanistic explanations of development are possible or whether alternative explanatory principles or even vital forces need to be assumed. In particular, the demonstrated ability of embryonic cells to tune their developmental fate precisely to their relative position and the overall size of the embryo was once thought to be inexplicable in mechanistic terms. Taking a causal perspective, this Element examines to what extent and how (...) class='Hi'>developmental biology, having turned molecular about four decades ago, has been able to meet the vitalist challenge. It focuses not only on the nature of explanations but also on the usefulness of causal knowledge – including the knowledge of classical experimental embryology – for further scientific discovery. It also shows how this causal perspective allows us to understand the nature and significance of some key concepts, including organizer, signal and morphogen. This title is also available as Open Access on Cambridge Core. (shrink)

The present paper analyzes the use and understanding of the homology concept across different biological disciplines. It is argued that in its history, the homology concept underwent a sort of adaptive radiation. Once it migrated from comparative anatomy into new biological fields, the homology concept changed in accordance with the theoretical aims and interests of these disciplines. The paper gives a case study of the theoretical role that homology plays in comparative and evolutionary biology, in molecular biology, (...) and in evolutionary developmental biology. It is shown that the concept or variant of homology preferred by a particular biological field is used to bring about items of biological knowledge that are characteristic for this field. A particular branch of biology uses its homology concept to pursue its specific theoretical goals. (shrink)

Alexander Rosenberg recently claimed (1997) that developmental biology is currently being reduced to molecular biology. cite several concrete biological examples that are intended to impugn Rosenberg's claim. I first argue that although Laubichler and Wagner's examples would refute a very strong reductionism, a more moderate reductionism would escape their attacks. Next, taking my cue from the antireductionist's perennial stress on the importance of spatial organization, I describe one form an empirical finding that refutes this moderate reductionism (...) would take. Finally, I point out an actual example, anterior-posterior axis determination in the chick, that challenges the reductionist's belief that all developmental regularities can be explained by molecular biology. In short, I argue that Rosenberg's position can be saved from Laubichler and Wagner's criticisms and putative counter-examples, but it would not survive a different kind of counter-example. (shrink)

Developmental biology is the science of explaining how a variety of interacting processes generate the heterogeneous shapes, size, and structural features of an organism as it develops rom embryo to adult, or more generally throughout its life cycle (Love, 2008b; Minelli, 2011a). Although it is commonplace in philosophy to associate sciences with theories such that the individuation of a science is dependent on a constitutive theory or group of models, it is uncommon to find presentations of developmental (...) biology making reference to a theory or theories of development. For example, in the third edition of Essential Developmental Biology (Slack, 2013), three families of approaches are described (developmental genetics, experimental embryology, and molecular and cell biology), and the appendix contains a catalogue of ‘key molecular components’ (genes, transcription factor, families, inducing factor families, cytoskeleton, cell adhesion molecules, and extracellular matrix components); however, no standard theory or group of models provides a theoretical scaffolding to the book nor is any mentioned. (shrink)

Model organisms became an indispensable part of experimental systems in molecular developmental and cell biology, constructed to investigate physiological and pathological processes. They are thought to play a crucial role for the elucidation of gene function, complementing the sequencing of the genomes of humans and other organisms. Accordingly, historians and philosophers paid considerable attention to various issues concerning this aspect of experimental biology. With respect to the representational features of model organisms, that is, their status as (...) models, the main focus was on generalization of phenomena investigated in such experimental systems. Model organisms have been said to be models for other organisms or a higher taxon. This, however, presupposes a representation of the phenomenon in question. I will argue that prior to generalization, model organisms allow researchers to built generative material models of phenomena – structures, processes or the mechanisms that explain them – through their integration in experimental set-ups that carve out the phenomena from the whole organism and thus represent them. I will use the history of zebrafish biology to show how model organism systems, from around 1970 on, were developed to construct material models of molecular mechanisms explaining developmental or physiological processes. (shrink)

Evolutionary developmental biology (evo-devo) has undergone dramatic transformations since its emergence as a distinct discipline. This paper aims to highlight the scope, power, and future promise of evo-devo to transform and unify diverse aspects of biology. We articulate key questions at the core of eleven biological disciplines—from Evolution, Development, Paleontology, and Neurobiology to Cellular and Molecular Biology, Quantitative Genetics, Human Diseases, Ecology, Agriculture and Science Education, and lastly, Evolutionary Developmental Biology itself—and discuss why (...) evo-devo is uniquely situated to substantially improve our ability to find meaningful answers to these fundamental questions. We posit that the tools, concepts, and ways of thinking developed by evo-devo have profound potential to advance, integrate, and unify biological sciences as well as inform policy decisions and illuminate science education. We look to the next generation of evolutionary developmental biologists to help shape this process as we confront the scientific challenges of the 21st century. (shrink)

Despite the productivity of basic cancer research, cancer continues to be a health burden to society because this research has not yielded corresponding clinical applications. Many proposed solutions to this dilemma have revolved around implementing organizational and policy changes related to cancer research. Here I argue for a different solution: a new conceptualization of causation in cancer. Neither the standard molecular biomarker approaches nor evolutionary biology approaches to cancer fully capture its complex causal dynamics, even when considered jointly. (...) These approaches map on to Ernst Mayr’s proximate–ultimate distinction, which is an inadequate conceptualization of causation in biological systems and makes it difficult to connect developmental and evolutionary viewpoints. I propose looking to evolutionary developmental biology to overcome the distinction and integrate the proximate and ultimate causal frameworks. I use the concepts of modularity and evolvability to show how an EvoDevo perspective can be manifested in cancer translational research. This perspective on causation in cancer is better suited for integrating the complexity of current empirical results and can facilitate novel developments in the investigation and clinical treatment of cancer. (shrink)

The successes of molecular developmental biology over the last ten years have been particularly impressive in those directions favored by its major paradigms. New technologies have both guided and been guided by the progress of the field. I review briefly some of the major insights into embryonic development that have derived from research in four specific areas: early embryogenesis of various forms; “pattern formation”; evolutionary conservation of regulatory elements; and spatial mechanisms of gene regulation. There remain many (...) major problem areas, some of which may require new orientations to solve. (shrink)

An exploration of the nexus between ecology, evolutionary biology and molecular biology, via the concept of phenotypic plasticity.

After the discovery of the structure of DNA in 1953, scientists working in molecular biology embraced reductionism—the theory that all complex systems can be understood in terms of their components. Reductionism, however, has been widely resisted by both nonmolecular biologists and scientists working outside the field of biology. Many of these antireductionists, nevertheless, embrace the notion of physicalism—the idea that all biological processes are physical in nature. How, Alexander Rosenberg asks, can these self-proclaimed physicalists also be antireductionists? (...) With clarity and wit, Darwinian Reductionism navigates this difficult and seemingly intractable dualism with convincing analysis and timely evidence. In the spirit of the few distinguished biologists who accept reductionism—E. O. Wilson, Francis Crick, Jacques Monod, James Watson, and Richard Dawkins—Rosenberg provides a philosophically sophisticated defense of reductionism and applies it to molecular developmental biology and the theory of natural selection, ultimately proving that the physicalist must also be a reductionist. (shrink)

Sponges branch basally in the metazoan phylogenetic tree and are believed to be composed of four distinct lineages with still uncertain relationships. Indeed, some molecular studies propose that Homoscleromorpha may be a fourth Sponge lineage, distinct from Demospongiae in which they were traditionally classified. They harbour many features that distinguish them from other sponges and are more evocative of those of the eumetazoans. They are notably the only sponges to possess a basement membrane with collagen IV and specialized cell‐junctions, (...) thus possessing true epithelia. Among Homoscleromorphs, we have chosen Oscarella lobularis as a model species. This common and easily accessible sponge is characterized by relatively simple histology and cell composition, absence of skeleton, and strongly pronounced epithelial structure. In this review, we explore the specific features that make O. lobularis a promising homoscleromorph sponge model for evolutionary and developmental researches. (shrink)

Despite the transformation in biological practice and theory brought about by discoveries in molecular biology, until recently philosophy of biology continued to focus on evolutionary biology. When the Human Genome Project got underway in the late 1980s and early 1990s, philosophers of biology -- unlike historians and social scientists -- had little to add to the debate. In this landmark collection of essays, Sahotra Sarkar broadens the scope of current discussions of the philosophy of (...) class='Hi'>biology, viewing molecular biology as a unifying perspective on life that complements that of evolutionary biology. His focus is on molecular biology, but the overriding question behind these papers is what molecular biology contributes to all traditional areas of biological research.Molecular biology -- described with some foresight in a 1938 Rockefeller Foundation report as a branch of science in which "delicate modern techniques are being used to investigate ever more minute details" -- and its modeling strategies apparently argue in favor of physical reductionism. Sarkar's first three chapters explore reductionism -- defending it, but cautioning that reduction to molecular interactions is not necessarily a reduction to genetics. The next sections of the book discuss function, exploring how functional explanations pose a problem for reductionism; the informational interpretation of biology and how it interacts with reductionism; and the tension between the unifying framework of molecular biology and the received framework of evolutionary theory. The concluding chapter is an essay in the emerging field of developmental evolution, exploring what molecular biology may contribute to the transformation of evolutionary theory as evolutionary theory takes into account morphogenetic development. (shrink)

The convergence of developmental biology — embryology — and molecular biology was one of the major scientific events of the last decades of the twentieth century. The transformation of developmental biology by the concepts and methods of molecular biology has already been described. Less has been told on the reciprocal transformation of molecular biology on contact with higher organisms. The transformation of molecular biology occurred at the end of (...) a deep crisis which affected this discipline in the sixties and seventies and which led to a cruel criticism of the preexisting models of gene regulation. Numerous new, sometimes heterodox, models were proposed to describe the level at which gene regulation took place and its underlying mechanisms. The crisis resolved itself at the beginning of the eighties with the rapid accumulation of results from genetic engineering techniques and, above all, a displacement of the descriptive level from the molecule to the cell. This displacement gave molecular biologists the 'explanandum' which had been cruelly lacking during their initial study of higher organisms. The new molecular cell biology is an interfield explanation of living phenomena, relating a description and an interpretation localized at different levels of organization. (shrink)

Fanconi anaemia (FA) comprises a group of autosomal recessive disorders resulting from mutations in one of eight genes (FANCA, FANCB, FANCC, FANCD1, FANCD2, FANCE, FANCF and FANCG). Although caused by relatively simple mutations, the disease shows a complex phenotype, with a variety of features including developmental abnormalities and ultimately severe anaemia and/or leukemia leading to death in the mid teens. Since 1992 all but two of the genes have been identified, and molecular analysis of their products has revealed (...) a complex mode of action. Many of the proteins form a nuclear multisubunit complex that appears to be involved in the repair of double‐strand DNA breaks. Additionally, at least one of the proteins, FANCC, influences apoptotic pathways in response to oxidative damage. Further analysis of the FANC proteins will provide vital information on normal cell responses to damage and allow therapeutic strategies to be developed that will hopefully supplant bone marrow transplantation. BioEssays 24:439–448, 2002. © 2002 Wiley Periodicals, Inc. (shrink)

Thomas Kuhn described the progress of science as comprising occasional paradigm shifts separated by interludes of ‘normal science’. The paradigm that has held sway since the inception of molecular biology is that genes (mainly) encode proteins. In parallel, theoreticians posited that mutation is random, inferred that most of the genome in complex organisms is non‐functional, and asserted that somatic information is not communicated to the germline. However, many anomalies appeared, particularly in plants and animals: the strange genetic phenomena (...) of paramutation and transvection; introns; repetitive sequences; a complex epigenome; lack of scaling of (protein‐coding) genes and increase in ‘noncoding’ sequences with developmental complexity; genetic loci termed ‘enhancers’ that control spatiotemporal gene expression patterns during development; and a plethora of ‘intergenic’, overlapping, antisense and intronic transcripts. These observations suggest that the original conception of genetic information was deficient and that most genes in complex organisms specify regulatory RNAs, some of which convey intergenerational information. Also see the video abstract here: https://youtu.be/qxeGwahBANw. (shrink)

Conrad Hal Waddington was a British developmental biologist who mainly worked in Cambridge and Edinburgh, but spent the late 1930s with Morgan in California learning about Drosophila. He was the first person to realize that development depended on the then unknown activities of genes, and he needed an appropriate model organism. His major experimental contributions were to show how mutation analysis could be used to investigate developmental mechanisms in Drosophila, and to explore how developmental mutation could drive (...) evolution, his other deep interest. Waddington was, however, predominantly a thinker, and set out to provide a coherent framework for understanding the genetic bases of embryogenesis and evolution, developing his ideas in many books. Perhaps his best-known concept is the epigenetic landscape: here a ball rolls down a complex valley, making path choices. The rolling ball represents a cell’s development over time, while the topography represents the changing regulatory environment that controls these choices. In its later forms, the role of each feature in the landscape was controlled by the effects of sets of interacting genes, an idea underpinning contemporary approaches to systems biology. Waddington was the first developmental geneticist and probably the most important developmental biologist of the pre-molecular age. (shrink)

Ongoing empirical discoveries in molecular biology have generated novel conceptual challenges and perspectives. Philosophers of biology have reacted to these trends when investigating the practice of molecular biology and contributed to scientific debates on methodological and conceptual matters. This article reviews some major philosophical issues in molecular biology. First, philosophical accounts of mechanistic explanation yield a notion of explanation in the context of molecular biology that does not have to rely on (...) laws of nature and comports well with molecular discovery. Second, reductionism continues to be debated and increasingly be rejected by scientists. Philosophers have likewise moved away from reduction toward integration across fields or integrative explanations covering several levels of organization. Third, although the gene concept has undergone substantial transformation and even fragmentation, it still enjoys widespread use by molecular biologists, which has prompted philosophers to understand the empirical reasons for this. At the same time, it has been argued the notion of ‘genetic information’ is largely an empty metaphor, which generates the illusion of explanatory understanding without offering an adequate explanation of molecular and developmental mechanisms. (shrink)

“Functional homology” appears regularly in different areas of biological research and yet it is apparently a contradiction in terms—homology concerns identity of structure regardless of form and function. I argue that despite this conceptual tension there is a legitimate conception of ‘homology of function’, which can be recovered by utilizing a distinction from pre-Darwinian physiology (use versus activity) to identify an appropriate meaning of ‘function’. This account is directly applicable to molecular developmental biology and shares a connection (...) to the theme of hierarchy in homology. I situate ‘homology of function’ within existing definitions and criteria for structural assessments of homology, and introduce a criterion of ‘organization’ for judging function homologues, which focuses on hierarchically interconnected interdependencies (similar to relative position and connection for skeletal elements in structural homology). This analysis of biological concepts has at least three broad philosophical consequences: (1) it provides the grounds for the study of behavior and psychological categories as homologues; (2) it demonstrates that philosophers who take selected effect function as primary effectively ignore large portions of comparative, structural, and experimental research, thereby misconstruing biological reasoning and knowledge; and, (3) it underwrites causal generalizations, which illuminates inferences made from model organisms in experimental biology. (shrink)

Based on a conference on the nature and origin of biological information held at Cornell University in 2011, this edited volume presents new research by experts in information theory, computer science, numerical simulation, thermodynamics, evolutionary theory, whole organism biology, developmental biology, molecular biology, genetics, physics, biophysics, mathematics, and linguistics.

All epistemic agents physically consist of parts that must somehow comprise an integrated cognitive self. Biological individuals consist of subunits (organs, cells, molecular networks) that are themselves complex and competent in their own context. How do coherent biological Individuals result from the activity of smaller sub-agents? To understand the evolution and function of metazoan bodies and minds, it is essential to conceptually explore the origin of multicellularity and the scaling of the basal cognition of individual cells into a coherent (...) larger organism. In this paper I synthesize ideas in cognitive science, evolutionary biology, and developmental physiology toward a hypothesis about the origin of Individuality: “Scale-Free Cognition”. I propose a fundamental definition of an Individual based on the ability to pursue goals at an appropriate level of scale and organization, and suggest a formalism for defining and comparing the cognitive capacities of highly diverse types of agents. Any Self is demarcated by a computational surface – the spatio-temporal boundary of events that it can measure, model, and try to affect. This surface sets a functional boundary - a cognitive “light cone” which defines the scale and limits of its cognition. I hypothesize that higher-level goal-directed activity and agency, resulting in larger cognitive boundaries, evolve from the primal homeostatic drive of living things to reduce stress – the difference between current conditions and life-optimal conditions. The mechanisms of developmental bioelectricity - the ability of all cells to form electrical networks that process information - suggests a plausible set of gradual evolutionary steps that naturally lead from physiological homeostasis in single cells to memory, prediction, and ultimately complex cognitive agents, via scale-up of the drive of infotaxis. Recent data on the molecular mechanisms of pre-neural bioelectricity suggest a model of how increasingly sophisticated cognitive functions emerge smoothly from cell-cell communication used to guide embryogenesis and regeneration. This set of hypotheses provides a novel perspective on numerous phenomena, such as cancer, and makes several unique, testable predictions for interdisciplinary research that have implications not only for evolutionary developmental biology but also for biomedicine and perhaps artificial intelligence and exobiology. (shrink)

Between November 30th and December 2nd, 2015, the Jacques Loeb Centre for the History and Philosophy of the Life Sciences at Ben-Gurion University of the Negev in Beer Sheva held its Eighth International Workshop under the title “From Genome to Gene: Causality, Synthesis and Evolution”. Eric Davidson, the founder of the concept of developmental Gene Regulatory Networks, had regularly attended the previous meetings, and his participation in this one was expected, but he suddenly passed away 3 months before. In (...) this paper, we provide an introduction and overview on five papers that were presented at the workshop and examine the importance of genomes and gene regulatory networks in extant biology, developmental biology, evolutionary biology and medicine, as well as a collection of remembrances of Eric Davidson, of his personality as well as of his scientific contributions. Historical perspectives are provided, and the ethical issues raised by the new tools developed to modify the genome are also discussed. (shrink)

This paper argues that the consensus physicalist antireductionism in the philosophy of biology cannot accommodate the research strategy or indeed the recent findings of molecular developmental biology. After describing Wolperts programmatic claims on its behalf, and recent work by Gehring and others to identify the molecular determinants of development, the paper attempts to identify the relationship between evolutionary and developmental biology by reconciling two apparently conflicting accounts of bio-function – Wrights and Nagels (as (...) elaborated by Cummins). Finally, the paper seeks a way of defending the two central theses of physicalist antireductionism in the light of the research program of molecular developmental biology, by sharply reducing their metaphysical force. (shrink)

Philosophy of Experimental Biology explores some central philosophical issues concerning scientific research in experimental biology, including genetics, biochemistry, molecular biology, developmental biology, neurobiology, and microbiology. It seeks to make sense of the explanatory strategies, concepts, ways of reasoning, approaches to discovery and problem solving, tools, models and experimental systems deployed by scientific life science researchers and also integrates developments in historical scholarship, in particular the New Experimentalism. It concludes that historical explanations of scientific change (...) that are based on local laboratory practice need to be supplemented with an account of the epistemic norms and standards that are operative in science. This book should be of interest to philosophers and historians of science as well as to scientists. (shrink)

Biologists and philosophers often use the language of determination in order to describe the nature of developmental phenomena. Accounts in terms of determination have often been reductionist. One common idea is that DNA is supposed to play a special explanatory role in developmental explanations, namely, that DNA is a developmental determinant. In this article we try to make sense of determination claims in developmental biology. Adopting a manipulationist approach, we shall first argue that the notion (...) of developmental determinant is causal. We suggest that two different theses concerning developmental determination can be articulated: determination of occurrence and structural determination. We shall argue that, while the first thesis is problematic, the second, opportunely qualified, is feasible. Finally, we shall argue that an analysis of biological causation in terms of determination cannot account for entangled dynamics. Characterising causal entanglement as a particular kind of interactive causation whereby difference-making causes ascribable to different levels of biological organisation influence a particular ontogenetic outcome, we shall, via two illustrative examples, diagnose some potential limits of a reductionist, molecular and intra-level understanding of biological causation. (shrink)

Molecular Weismannism is the claim that: “In the development of an individual, DNA causes the production both of DNA (genetic material) and of protein (somatic material). The reverse process never occurs. Protein is never a cause of DNA”. This principle underpins both the idea that genes are the objects upon which natural selection operates and the idea that traits can be divided into those that are genetic and those that are not. Recent work in developmental biology and (...) in philosophy of biology argues that an acceptance of Molecular Weismannism requires the tacit assumption that genetic causes are different in kind from other developmental causes. They argue that if this assumption proves to be unwarranted then we should abandon, not just gene selectionism and gene centred functional solutions to the units of selection problem, but also the very notion that there is any such thing as a “genetic trait”. A group of possible causal distinctions (proximity, ultimacy and specificity) are explored and found wanting. It is argued that an extended version of information theory, while not strong enough to support Molecular Weismannism, will support both the claim that traits can be divided into those that are genetic and those that are not as well as the claim that there is good reason to privilege genetic causes within evolutionary and developmental explanations. The outcome of this for the units of selection debate is explored. (shrink)

Neurobiologists talk of linking mind to molecular dynamics in and between neurons. Such talk is dismissed by cognitive scientists, including many cognitive neuroscientists, due to the number of “levels” that separate behaviors from these molecular events. In this paper I explain what neurobiologists mean by such claims by describing the kinds of experiment tools that have forged these linkages, directly on lab benches. I here focus on one of these tools, gene targeting techniques, brought into behavioral neuroscience from (...) developmental biology more than a quarter-century ago. Discussion of this tool does more than illuminate these claims by neurobiologists, however. An account of its development shows the doubly dependent role that theory plays in neurobiology. Our best current theories about “how the brain works” depend entirely on the experiment tools neuroscientists have available. And these tools get developed via the solution of engineering problems, not the application of theory. Theory is thus of tertiary importance in neuroscience, not of the primary importance that many cognitive scientists assume it to occupy. (shrink)

A strong motivation for the human genome project was to relate biological features to the structure and function of small sets of genes, and ideally to individual genes. However, it is now increasingly realized that many problems require a "systems" approach emphasizing the interplay of large numbers of genes, and the involvement of complex networks of gene regulation. This implies a new emphasis on integrative, systems theoretical approaches. It may be called 'holistic' if the term is used without irrational overtones, (...) in the general sense of directing attention to integrated features of organs and organisms. In the history of biology, seemingly conflicting reductionist and holistic notions have alternated, with bottom-up as well as top-down approaches eventually contributing to the solutions of basic problems. By now, there is no doubt that biological features and phenomena are rooted in physico-chemical processes of the molecules involved; and yet, integrated systems aspects are becoming more and more relevant in developmental biology, brain and behavioural science, and socio-biology. -/- . (shrink)

The ascidian embryo has long provided a model system for ‘mosaic’ development. This article reviews recent advances in the study of ascidian developmental biology. These include: (a) the re‐analysis of cell lineages in ascidian embryos with the ascertainment of developmental fates of every blastomere of a 110‐cell embryo; (b) the development of several tissue‐specific monoclonal antibodies; (c) the investigation and description of cell cycle requirements for differentiation; it has been found that neither cytokinesis nor nuclear division is (...) required for differentiation, but that several rounds of DNA replication are essential for the expression of certain tissue‐specific genes; and (d) the demonstration by new descriptive and experimental studies of the presence of cytoplasmic factors or determinants responsible for specification of embryonic cell features; myoplasm which is thought to contain muscle determinants has been isolated, and immunological attempts to elucidate the molecular nature of the factors have begun. (shrink)

In 1809--the year of Charles Darwin's birth--Jean-Baptiste Lamarck published Philosophie zoologique, the first comprehensive and systematic theory of biological evolution. The Lamarckian approach emphasizes the generation of developmental variations; Darwinism stresses selection. Lamarck's ideas were eventually eclipsed by Darwinian concepts, especially after the emergence of the Modern Synthesis in the twentieth century. The different approaches--which can be seen as complementary rather than mutually exclusive--have important implications for the kinds of questions biologists ask and for the type of research they (...) conduct. Lamarckism has been evolving--or, in Lamarckian terminology, transforming--since Philosophie zoologique's description of biological processes mediated by "subtle fluids." Essays in this book focus on new developments in biology that make Lamarck's ideas relevant not only to modern empirical and theoretical research but also to problems in the philosophy of biology. Contributors discuss the historical transformations of Lamarckism from the 1820s to the 1940s, and the different understandings of Lamarck and Lamarckism; the Modern Synthesis and its emphasis on Mendelian genetics; theoretical and experimental research on such "Lamarckian" topics as plasticity, soft (epigenetic) inheritance, and individuality; and the importance of a developmental approach to evolution in the philosophy of biology. The book shows the advantages of a "Lamarckian" perspective on evolution. Indeed, the development-oriented approach it presents is becoming central to current evolutionary studies--as can be seen in the burgeoning field of Evo-Devo. Transformations of Lamarckism makes a unique contribution to this research. (shrink)

Comprised of essays by top scholars in the field, this volume offers concise overviews of philosophical issues raised by biology. Brings together a team of eminent scholars to explore the philosophical issues raised by biology Addresses traditional and emerging topics, spanning molecular biology and genetics, evolution, developmental biology, immunology, ecology, mind and behaviour, neuroscience, and experimentation Begins with a thorough introduction to the field Goes beyond previous treatments that focused only on evolution to give (...) equal attention to other areas, such as molecular and developmental biology Represents both an authoritative guide to philosophy of biology, and an accessible reference work for anyone seeking to learn about this rapidly-changing field. (shrink)

Multilevel research strategies characterize contemporary molecular inquiry into biological systems. We outline conceptual, methodological, and explanatory dimensions of these multilevel strategies in microbial ecology, systems biology, protein research, and developmental biology. This review of emerging lines of inquiry in these fields suggests that multilevel research in molecular life sciences has significant implications for philosophical understandings of explanation, modeling, and representation.

The use of informational terms is widespread in molecular and developmental biology. The usage dates back to Weismann. In both protein synthesis and in later development, genes are symbols, in that there is no necessary connection between their form (sequence) and their effects. The sequence of a gene has been determined, by past natural selection, because of the effects it produces. In biology, the use of informational terms implies intentionality, in that both the form of the (...) signal, and the response to it, have evolved by selection. Where an engineer sees design, a biologist sees natural selection. (shrink)

There are two fundamentally distinct kinds of biological theorizing. "Formal biology" focuses on the relations, captured in formal laws, among mathematically abstracted properties of abstract objects. Population genetics and theoretical mathematical ecology, which are cases of formal biology, thus share methods and goals with theoretical physics. "Compositional biology," on the other hand, is concerned with articulating the concrete structure, mechanisms, and function, through developmental and evolutionary time, of material parts and wholes. Molecular genetics, biochemistry, (...) class='Hi'>developmental biology, and physiology, which are examples of compositional biology, are in serious need of philosophical attention. For example, the very concept of a "part" is understudied in both philosophy of biology and philosophy of science. ;My dissertation is an attempt to clarify the distinction between formal biology and compositional biology and, in so doing, provide a clear philosophical analysis, with case studies, of compositional biology. Given the social, economic, and medical importance of compositional biology, understanding it is urgent. For my investigation, I draw on the philosophical fields of metaphysics and epistemology, as well as philosophy of biology and philosophy of science. I suggest new ways of thinking about some classic philosophy of science issues, such as modeling, laws of nature, abstraction, explanation, and confirmation. I hint at the relevance of my study of two kinds of biological theorizing to debates concerning the disunity of science. (shrink)

In 1948, a dynamic junior member of the Johns Hopkins Biology Department, William McElroy, became the first director of the McCollum—Pratt Institute for the Investigation of Micronutrient Elements. The Institute was founded at the university to further studies into the practicalities of animal nutrition. Ultimately, however, the Institute reflected McElroy's vision that all biological problems, including nutrition, could be best investigated through basic biochemical and enzymes studies. The Institute quickly became a hub of biochemical research over the following decade, (...) producing foundational work on metabolism and a respected series of symposia. In this paper, I argue that McElroy's biochemical vantage on biology also permeated the traditionally morphological and embryological Biology Department at Hopkins. Largely due to the activity of McElroy and the Institute, the faculty, course offerings, and research underwent a radical reorientation toward biochemistry and molecular biology in the 1950s, even while maintaining a commitment to developmental biology. While the history of postwar biology is often told as the ascendancy of the "new" biology over "traditional" biology, the case of McElroy and the McCollum—Pratt Institute affords an opportunity for historical examination of biochemical and molecular science as a lens through which all branches of biology at an institution were reconceived and unified. (shrink)

In recent years, a proliferation of books about empathy, cooperation and pro-social behaviours (Brooks, 2011a) has significantly influenced the discourse of the life-sciences and reversed consolidated views of nature as a place only for competition and aggression. In this article I describe the recent contribution of three disciplines – moral psychology (Jonathan Haidt), primatology (Frans de Waal) and the neuroscience of morality – to the present transformation of biology and evolution into direct sources of moral phenomena, a process here (...) named the ‘moralization of biology’. I conclude by addressing the ambivalent status of this constellation of authors, for whom today ‘morality comes naturally’: I explore both the attractiveness of their message, and the problematic epistemological assumptions of their research programmes in the light of new discoveries in developmental and molecular biology. (shrink)

The nature/nurture debate is not dead. Dichotomous views of development still underlie many fundamental debates in the biological and social sciences. Developmental systems theory offers a new conceptual framework with which to resolve such debates. DST views ontogeny as contingent cycles of interaction among a varied set of developmental resources, no one of which controls the process. These factors include DNA, cellular and organismic structure, and social and ecological interactions. DST has excited interest from a wide range of (...) researchers, from molecular biologists to anthropologists, because of its ability to integrate evolutionary theory and other disciplines without falling into traditional oppositions. The book provides historical background to DST, recent theoretical findings on the mechanisms of heredity, applications of the DST framework to behavioral development, implications of DST for the philosophy of biology, and critical reactions to DST. (shrink)

The Human Genome Project is nearing completion, and shortly we will have access to the complete genetic sequence of an average human being. Hopes are high that the sequence will contribute profoundly to medicine in particular, but also to our understanding of our evolutionary past. Of course, detractors have long insisted that because the HGP represents a victory for formalism in biology, determining the function of DNA sequences will remain an outstanding problem for at least the next several decades. (...) Moreover, it is not clear that having the complete sequence will be significantly useful to biologists seeking to understand gene function in the first place. What can we expect in the postgenomic era? ;I reject the very idea that a complete, encapsulated sequence of a human genome is foundational to biological understanding. I set my investigation within the framework of the ancient debate between preformationists and epigenecists. I survey and conceptually analyze arguments on both sides, especially as they relate to the separation of genetics and embryology in the early part of the twentieth century. I identify modern variants of both preformationism and epigenesis, and note their reconciliation in the form of a Modern Consensus on development established after the neo-Darwinian Synthesis in biology in the 1940s. ;Drawing on recent work in molecular and developmental biology, I challenge the seeming intuitiveness of the Modern Consensus and its subsumption of developmental concerns under the aegis of molecular genetics. I then propose and defend an alternative synthesis of preformationism and epigenesis, and of genetics and developmental biology, according to which development does not reduce to mere gene activation. I underscore the practical benefit of my perspective through a lengthy discussion of the psychiatric genetics approach to schizophrenia. (shrink)

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)

As a result of the time‐ and context‐dependency of gene expression, gene regulatory and signaling pathways undergo dynamic changes during development. Creating a model of the dynamics of molecular interaction networks offers enormous potential for understanding how a genome orchestrates the developmental processes of an organism. The dynamic nature of pathway topology calls for new modeling strategies that can capture transient molecular links at the runtime. The aim of this paper is to present a brief and informative, (...) but not all‐inclusive, viewpoint on the computational aspects of modeling and simulation of a non‐static molecular network. BioEssays 26:68–72, 2004. © 2003 Wiley Periodicals, Inc. (shrink)