Feminist critiques of science provide fertile ground for any investigation of the ways in which social influences may shape the content of science. Many authors working in this field are from the natural and social sciences; others are philosophers. For philosophers of science, recent work on sexist and androcentric bias in science raises hard questions about the extent to which reigning accounts of scientific rationality can deal successfully with mounting evidence that gender ideology has had deep (...) and extensive effects on the development of many scientific disciplines.Feminist critiques of biology have been especially important in the political struggle for gender equality because biologically determinist arguments are so often cited to ‘explain’ women’s oppression. They explain why it is ‘natural’ for women to function in a socially subordinate role, why men are smarter and more aggressive than women, why women are destined to be homebodies, and why men rape. (shrink)

A good division of biology is important for clarity of thought, presentation of the problems and nowadays also for science policy. Various classifications are in use, depending upon different parameters. A division can be based on objects and on aspects. A modern classification on objects is based on the levels of organisation. Methodological principles play a role in the background.

Many studies of the unification of science focus on the theories of different disciplines. The model for integration is the theory reduction model. This paper argues that the embodiment of theories in scientists, and the institutions in which scientists work and the instruments they employ, are critical to the sort of integration that actually occurs in science. This paper examines the integration of scientific endeavors that emerged in cell biology in the period after World War II when (...) the development of cell fractionation and electron microscopy made serious investigations of cell organelles possible. One surprising feature of such integration is that it generated further disintegration as the new institutions of cell biology separated the practitioners of the new discipline from other, closely related biological disciplines. (shrink)

Do the sciences aim to uncover the structure of nature, or are they ultimately a practical means of controlling our environment? In Instrumental Biology, or the Disunity of Science, Alexander Rosenberg argues that while physics and chemistry can develop laws that reveal the structure of natural phenomena, biology is fated to be a practical, instrumental discipline. Because of the complexity produced by natural selection, and because of the limits on human cognition, scientists are prevented from uncovering the basic structure (...) of biological phenomena. Consequently, biology and all of the disciplines that rest upon it--psychology and the other human sciences--must aim at most to provide practical tools for coping with the natural world rather than a complete theoretical understanding of it. (shrink)

In this paper I respond to Wim van der Steen''s arguments against the supposed current overemphasis on norms ofcoherence andinterdisciplinary integration in biology. On the normative level, I argue that these aremiddle-range norms which, although they may be misapplied in short-term attempts to solve (temporarily?) intractable problems, play a guiding role in the longer-term treatment of biological problems. This stance is supported by a case study of apartial success story, the development of the one gene — one enzyme hypothesis. (...) As that case shows, thegoal of coherent interdisciplinary integration not only provides guidance for research, but also provides the standard for recognizingfailed integrations of the sort that van der Steen criticizes. (shrink)

In the last few years, biologists and computer scientists have claimed that the introduction of data science techniques in molecular biology has changed the characteristics and the aims of typical outputs (i.e. models) of such a discipline. In this paper we will critically examine this claim. First, we identify the received view on models and their aims in molecular biology. Models in molecular biology are mechanistic and explanatory. Next, we identify the scope and aims of data science (machine (...) learning in particular). These lie mainly in the creation of predictive models which performances increase as data set increases. Next, we will identify a tradeoff between predictive and explanatory performances by comparing the features of mechanistic and predictive models. Finally, we show how this a priori analysis of machine learning and mechanistic research applies to actual biological practice. This will be done by analyzing the publications of a consortium—The Cancer Genome Atlas—which stands at the forefront in integrating data science and molecular biology. The result will be that biologists have to deal with the tradeoff between explaining and predicting that we have identified, and hence the explanatory force of the ‘new’ biology is substantially diminished if compared to the ‘old’ biology. However, this aspect also emphasizes the existence of other research goals which make predictive force independent from explanation. (shrink)

The quality of doctoral-level biochemistry (N=139), botany (N=83), cellular/molecular biology (N=89), microbiology (N=134), physiology (N=101), and zoology (N=70) programs at United States universities was assessed, using 16 measures. These measures focused on variables related to: (1) program size; (2) characteristics of graduates; (3) reputational factors (scholarly quality of faculty, effectiveness of programs in educating research scholars/scientists, improvement in program quality during the last 5 years); (4) university library size; (5) research support; and (6) publication records. Chapter I discusses prior attempts (...) to assess quality in graduate education, development of the study plans, and the selection of disciplines and programs to be evaluated. Chapter II discusses the methodology used, focusing on each of the assessment measures. Chapters III to VIII present, respectively, findings from the analyses of the biochemistry, botany, cellular/molecular biology, microbiology, physiology, and zoology programs. Chapter IX includes a summary of results, correlations among measures, several additional analyses, and suggestions for future studies. Among the findings reported are those indicating that cellular/molecular biology programs had, on the average, the largest number of faculty and that students in cellular/molecular biology, biology, biochemistry, microbiology, and physiology received a relatively high fraction of financial support. (Survey instruments and supporting documentation are included in appendices.) (JN). (shrink)

Woodger first gives a rough account of the "Boole-Frege" movement in modern logic and persuasively argues as to the importance of formalized language-systems for the methodology of science. Some of these arguments are as follows: A natural language such as English, he notes, "is not only used for purposes of communication in the scientific sense. It is also used for the writing of poetry, for religious devotion, for political controversy, and for persuading people to buy some of the products (...) of industrial activity which they would not otherwise want. But these pursuits make demands upon language which are very different from those made by science. The requirements of science prove on investigation to be quite surprisingly meagre and the excessive riches of a natural language like English are a source of embarrassment. They tempt us to employ linguistic devices borrowed from extra-scientific usages which can have unfortunate consequences. Metaphors, for example, with which some branches of biology abound, are often suggestive and may be harmless enough if they are recognized for what they are. But at best they are makeshifts and substitutes for genuine biological statements, and the fact that recourse is had to them is surely a sign of immaturity. Science demands great linguistic austerity and discipline, and the canons of good style in scientific writing are different from those of good writing in other kinds of literature." Another argument is that "sooner or later the linguistic habits of everyday life will cease to do justice to... the... increasing complexity and novelty of observation and hypothesis." A third argument is that scientific language is used not only for the purpose of communication, for recording observations, or for formulating general laws or hypotheses. It is also used for calculation and the unearthing of the consequences of our assumptions. The logic underlying a formalized language is explicitly designed to enable us to calculate easily and efficiently. The important, and now thoroughly established, methodological distinction between object-language and meta-language is blurred for natural language and is best maintained in terms of formalized language-systems. And, finally, in natural language the important distinction between syntax and semantics also tends to be blurred. "From both the syntactical and the semantical points of view natural languages are incredibly complicated and unruly. The rules of ordinary gram mar are quite insufficient from the standpoint of the requirements of science, and the problems connected with meaning and truth in relation to natural languages are enormously complicated and perhaps insoluble.". (shrink)

Historians agree that the second half of the twentieth century saw widespread changes in the structure of biological science in universities. This shift was, and continues to be, characterized by the de-differentiation of nineteenth and early twentieth century disciplines, with increasing emphasis on the methods and authority of molecular fields. Yet we currently lack appreciation of the dynamics that underpinned these changes, and of their tangible effects on the working practices of those involved. In this article we (...) examine the wholesale reform of biological science at the University of Manchester, England, that occurred in two successive steps in 1986 and 1993. We examine how reform was enabled by economic and political factors, as staff seized upon national pressures; in so doing, we emphasize how this reform was shaped by a generational view of the biological sciences as a one field, unified by molecular techniques. We assess how the success of these reforms was tied to new management policies that rewarded research activity in molecular fields, and refigured teaching as a punishment for research inactivity. We close by showing how our analysis fits amongst, and can contribute to, ‘big picture’ debates in the history and sociology of knowledge. (shrink)

This paper focuses on a running dispute between Werner Callebaut’s naturalistic view and Filip Kolen and Gertrudis Van de Vijver’s transcendentalist view on the nature of philosophy of biology and the relation of this discipline to biological sciences. It is argued that, despite differences in opinion, both positions agree that philosophy of biology’s ultimate goal is to ‘move’ biology or at least be ‘meaningful’ to it. In order to make this goal clear and effective, more is needed than a (...) polarizing debate which hardly touches upon biology. Therefore, a redirection in discussion is suggested towards a reflection on the possibilities of incorporating philosophy in interdisciplinary research, and on finding concrete research questions which are of interest both to the philosopher and to the biologist. (shrink)

This paper focuses on a running dispute between Werner Callebaut’s naturalistic view and Filip Kolen and Gertrudis Van de Vijver’s transcendentalist view on the nature of philosophy of biology and the relation of this discipline to biological sciences. It is argued that, despite differences in opinion, both positions agree that philosophy of biology’s ultimate goal is to ‘move’ biology or at least be ‘meaningful’ to it. In order to make this goal clear and effective, more is needed than a (...) polarizing debate which hardly touches upon biology. Therefore, a redirection in discussion is suggested towards a reflection on the possibilities of incorporating philosophy in interdisciplinary research, and on finding concrete research questions which are of interest both to the philosopher and to the biologist. (shrink)

The sciences may be conceptualized as a hierarchy ranked by level of organization (e.g., many‐body physics ranks above particle physics). Each science serves as an antidiscipline for the science above it; that is, between each pair, tense but creative interplay is inevitable. Biology has advanced through such tension between its subdisciplines and now can serve as an antidiscipline for the social sciences—for anthropology, for example, by examining the connection between cultural and biological evolution; for psychology, by addressing (...) the nature of learning and the structure of the unconscious; for economics, by examining economically irrational behavior and by comparing economic activity in humans and other species. Sociology, concerned mainly with advanced literate societies, is relatively remote from the genetic basis of human social behavior. However, moving between biological and social levels of organization generates richness and points to new and unexpected principles. (shrink)

The influence that philosophy of science has had on scientific practice is as controversial as it is undeniable, especially in the case of biology. The dynamic between philosophy and biology as disciplines has developed along two different lines that can be characterized as 'paternal', on the one hand, and more 'fraternal', on the other. The role Popperian principles of demarcation and falsifiability have played in both the systematics community as well as the ongoing evolution-creation debates illustrate these contrasting (...) forms of interdisciplinary engagement, underscoring the influence philosophy of science in shaping our contemporary understanding of biology in the North American context. However, a strict disciplinary distinction between philosophy and science may itself be a false dichotomy that risks hampering future development of the biological sciences. By actively engaging with philosophical considerations as an integral part of their scientific practice, nineteenth-century biologists offer an interesting counterpoint to current trends of overspecialization and provide a model of scientists who avoided extremes of antagonism with, or subservience to, philosophy. (shrink)

This collection of revised and new essays argues that biology is an autonomous science rather than a branch of the physical sciences. Ernst Mayr, widely considered the most eminent evolutionary biologist of the 20th century, offers insights on the history of evolutionary thought, critiques the conditions of philosophy to the science of biology, and comments on several of the major developments in evolutionary theory. Notably, Mayr explains that Darwin's theory of evolution is actually five separate theories, each with (...) its own history, trajectory and impact. Ernst Mayr, commonly referred to as the "Darwin of the 20th century" and listed as one of the top 100 scientists of all-time, is Professor Emeritus at Harvard University. What Makes Biology Unique is the 25th book he has written during his long and prolific career. His recent books include This is Biology: The Science of the Living World (Belknap Press, 1997) and What Evolution Is (Basic Books, 2002). (shrink)

Humanity’s self-ordained mandate to subdue and dominate nature is part of the cognitive foundation of the modern world—a perspective that remains deeply ingrained in science and technology. Marine biology has not been immune to this anthropocentric bias. But this needs to change, and the gaps between basic scientific disciplines and the global conservation imperatives of our time need to be bridged. In the face of a looming ecological and climate crisis, marine biologists must upgrade their values and professional (...) standards and help foster the radical transformation needed to avert a climate and ecological breakdown. To prevent some of the damage, they must cross the imaginary line that separates science from science-based activism and consciously pursue the health and durability of human and natural communities. To this end, they can (1) develop compelling narratives that engage human society, with emphasis on care for the wild living world; (2) move beyond marine conservation on paper and avoid self-serving complaisance; (3) advocate constructive changes in market and human behaviour, not only by documenting damage but also by clarifying how the extraction, production and consumption system can be steered away from practices that harm nature; (4) push for systemic change in politics through individual and collective efforts, supporting environmental activism and those who demand biosphere-saving policies; and (5) endorse a more ecocentric and holistic world vision, relinquishing contempt for spiritual wisdom and liaising with (or at least not dismissing) spiritual traditions that encourage equality, self-restraint and environmental sustainability. (shrink)

Despite the multidisciplinary dimension of the kinds of research conducted under the umbrella of synthetic biology, the US-based founders of this new research area adopted a disciplinary profile to shape its institutional identity. In so doing they took inspiration from two already established fields with very different disciplinary patterns. The analogy with synthetic chemistry suggested by the term ‘synthetic biology’ is not the only model. Information technology is clearly another source of inspiration. The purpose of the paper, with its focus (...) on the US context, is to emphasize the diversity of views and agendas coexisting under the disciplinary label synthetic biology, as the two models analysed are only presented as two extreme postures in the community. The paper discusses the question: in which directions the two models shape this emerging field? Do they chart two divergent futures for synthetic biology? (shrink)

I am honored to have been invited to participate in this Workshop on Comparative Studies of Building Molecular Biology, with a discussion of Japanese experiences in constructing a science — in this case, the discipline of molecular biology. As I understand it, the construction of a science must be equivalent to building a new culture. My having given this title to my paper suggests that I have enough knowledge about the subject to perhaps even extrapolate its course into (...) the future — which I do not. What I do have is a sincere admiration of my old friends and colleagues, in Japan and elsewhere, who together tried to build a new science of molecular biology in Japan. (shrink)

Research in ecology and evolutionary biology (evo-eco) often tries to emulate the “hard” sciences such as physics and chemistry, but to many of its practitioners feels more like the “soft” sciences of psychology and sociology. I argue that this schizophrenic attitude is the result of lack of appreciation of the full consequences of the peculiarity of the evo-eco sciences as lying in between a-historical disciplines such as physics and completely historical ones as like paleontology. Furthermore, evo-eco researchers have gotten (...) stuck on mathematically appealing but philosophi- cally simplistic concepts such as null hypotheses and p-values defined according to the frequentist approach in statistics, with the consequence of having been unable to fully embrace the complexity and subtlety of the problems with which ecologists and evolutionary biologists deal with. I review and discuss some literature in ecology, philosophy of science and psychology to show that a more critical methodological attitude can be liberating for the evo-eco scientist and can lead to a more fecund and enjoyable practice of ecology and evolutionary biology. With this aim, I briefly cover concepts such as the method of multiple hypotheses, Bayesian analysis, and strong inference. (shrink)

In this paper I first offer a systematic outline of a series of conceptual novelties in the life-sciences that have favoured, over the last three decades, the emergence of a more social view of biology. I focus in particular on three areas of investigation: (1) technical changes in evolutionary literature that have provoked a rethinking of the possibility of altruism, morality and prosocial behaviours in evolution; (2) changes in neuroscience, from an understanding of the brain as an isolated data processor (...) to the ultrasocial and multiply connected social brain of contemporary neuroscience; and (3) changes in molecular biology, from the view of the gene as an autonomous master of development to the ‘reactive genome’ of the new emerging field of molecular epigenetics. In the second section I reflect on the possible implications for the social sciences of this novel biosocial terrain and argue that the postgenomic language of extended epigenetic inheritance and blurring of the nature/nurture boundaries will be as provocative for neo-Darwinism as it is for the social sciences as we have known them. Signs of a new biosocial language are emerging in several social-science disciplines and this may represent an exciting theoretical novelty for twenty-first social theory. (shrink)

Explanation in biology has long been characterized as being very different from explanation in other scientific disciplines, very much so from explanation in physics. One of the reasons was the existence in biology of explanation types that were unheard of in the physical sciences: teleological explanations (e.g. Hull 1974), evolutionary explanations (e.g. Mayr 1988), or even functional explanations (e.g. Neander 1991). More recently, and owing much to the rise of molecular biology, biological explanations have been depicted as mechanisms (...) (e.g; Machamer, Darden and Craver 2000). The aim of this volume is to shed some new light on the diversity of explanation types in biology. What are the different types of explanation that occur in biology? Are these types of explanation specific to particular sub-disciplines of biology, or to particular types of problems across biology? How do they relate to each another? Do they compete with one another for answering the same questions? Or do they complement each other, providing insights to different questions? What are the reasons for such diversity? Can this diversity be overcome by a broader unifying model of explanation or is it more profound and irreducible? Why? This volume aims at making sense of this diversity of types of explanations that are found in biology, of their relationship with one another. After all, explanation in biology may prove not only different from explanation in the physical sciences, but also much more diverse than originally anticipated. (shrink)

In this essay, I build on the article by Soulé that established the foundation for the field of conservation biology. I analyze the presuppositions that have guided the discipline’s ethics in the 30 years since that article first appeared. I argue that conservation biology’s normative postulates introduced a paradigm shift that placed the diversity of the biota instead of the biota itself at the center of its ethics. I show that the ensuing priorities in the valuation of nature entail several (...) contradictions at the ethical level and are justifiable only through scientific postulates. Identifying potential revisions and latent ideological issues in science, I defend the position that such scientific legitimization of conservation measures becomes disputable when this option undermines the ethical status of non-human life. Furthermore, I explain the absence of social feedback regarding conservation measures from the perspective of this shift. I conclude with an invitation to critically rethink the ethical basis of conservation sciences so that these fields may achieve their intention of playing a key role in halting the destruction of nature and in encouraging society’s support. (shrink)

The life sciences have evoked long-standing philosophical debates on a system view of life versus a reductionist view that reduces the complexity of life-forms to parts-based entities that can be described purely mechanistically. This paper examines how current scientific advances in the life sciences can contribute to an anti-reductionist concept of life. It does so by looking at synthetic biology, a discipline within the life sciences that has an ambiguous relationship to this debate. While the field’s engineering approach to life (...) could be considered a manifestation of a reductionist view of life, it also builds on a more holistic, systems view of life. This paper analyses recent scientific practices taking place within synthetic biology that seem to challenge the reductionist view of life. After analyzing the main anti-reductionist philosophical accounts of life, I ask how synthetic biology practices can support these accounts of life by considering living systems as processual, collaborative, and cognitive, and life versus nonlife on a more gradual scale. This empirically informed paper contributes to the literature by drawing observations about the concept of life by connecting the following: the reductionist view in the life sciences, the different anti-reductionist metaphysical stances in the philosophy of biology, and the emerging practices in synthetic biology. The paper concludes that synthetic biology can support anti-reductionist views of life in the philosophy of biology. (shrink)

The biological functions debate is a perennial topic in the philosophy of science. In the first full-length account of the nature and importance of biological functions for many years, Justin Garson presents an innovative new theory, the 'generalized selected effects theory of function', which seamlessly integrates evolutionary and developmental perspectives on biological functions. He develops the implications of the theory for contemporary debates in the philosophy of mind, the philosophy of medicine and psychiatry, the philosophy of (...) biology, and biology itself, addressing issues ranging from the nature of mental representation to our understanding of the function of the human genome. Clear, jargon-free, and engagingly written, with accessible examples and explanatory diagrams to illustrate the discussion, his book will be highly valuable for readers across philosophical and scientific disciplines. (shrink)

Biology and history are often viewed as closely related disciplines, with biology informed by history, especially in its task of charting our evolutionary past. Maximizing the opportunities for cross-fertilization in these two fields requires an accurate reckoning of their commonalities and differences-precisely what this volume sets out to achieve. Specially commissioned essays by a team of recognized international researchers cover the full panoply of topics in these fields and include notable contributions on the correlativity of evolutionary and historical explanations, (...) applying to history the latest causal-mechanical approach in the philosophy of biology, and the question of generalized laws that might pertain across the two subjects. The collection opens with a vital interrogation of general issues on explanation that apart from potentially fruitful areas of interaction (could the etiology of the causal-mechanical perspective in biology account for the historical trajectory of the Roman Empire?) this volume also seeks to chart relative certainties distinguishing explanations in biology and history. It also assesses techniques such as the use of probabilities in biological reconstruction, deployed to overcome the inevitable gaps in physical evidence on early evolution. Methodologies such as causal graphs and semantic explanation receive in-depth analysis. Contributions from a host of prominent and widely read philosophers ensure that this new volume has the stature of a major addition to the literature. (shrink)

'A breath-taking panorama.' The Sunday Times 'Those seeking a grand overview of science's greatest hits over the past century will find it here.' The Washington Post 'Convincing... A provocative history probes the connections that are helping to unify scientific disciplines.... Watson examines an impressive array of connections... Whether you identify as a biologist, an astrophysicist, or a mathematician, one thing's for certain: We're all ultimately working with the same fabric.' Science 'Anyone interested in science will enjoy (...) this fascinating, fast-paced, intellectual journey through the history of scientific ideas. Watson masterfully weaves the concept of convergence through covering an astonishing breadth of scientific and cultural domains.' Mario Livio, astrophysicist, author of Brilliant Blunders and Why? Convergence is a history of modern science with an original and significant twist. Various scientific disciplines, despite their very different beginnings, and disparate areas of interest have been coming together over the past 150 years, converging and coalescing, to identify one extraordinary master narrative, one overwhelming interlocking coherent story: the history of the universe. Intimate connections between physics and chemistry have been revealed as have the links between quantum chemistry and molecular biology. Astronomy has been augmented by particle physics, psychology has been increasingly aligned with physics, with chemistry and even with economics. Genetics has been harmonised with linguistics, botany with archaeology, climatology with myth. This is a simple insight but one with profound consequences. Convergence is, as Nobel Prize-winning physicist Steven Weinberg has put it, 'The deepest thing about the universe.' This book does not, however, tell the story by beginning at the beginning and ending at the end. It is much more revealing, more convincing, and altogether more thrilling to tell the story as it emerged, as it began to fall into place, piece by piece, converging tentatively at first, but then with increasing speed, vigour and confidence. The overlaps and interdependence of the sciences, the emerging orderthat they are gradually uncovering, is without question the most enthralling aspect of twenty-first-century science. (shrink)

Animal welfare science and ecology are both generally concerned with the lives of animals, however they differ in their objectives and scope; the former studies the welfare of animals considered ‘domestic’ and under the domain of humans, while the latter studies wild animals with respect to ecological processes. Each of these approaches addresses certain aspects of the lives of animals living in the world though neither, we argue, tells us important information about the welfare of wild animals. This paper (...) argues for the development of a new scientific discipline ‘welfare biology’ to address these issues and more, given the deficiencies of pre-existing life science disciplines to research the subject. Welfare biology is the study of the welfare of all living beings who have a welfare, with a value orientation toward promoting that welfare, regardless of the beings’ situation or relationship to humans and our activities. (shrink)

As a discipline distinct from ecology, conservation biology emerged in the 1980s as a rigorous science focused on protecting biodiversity. Two algorithmic breakthroughs in information processing made this possible: place-prioritization algorithms and geographical information systems. They provided defensible, data-driven methods for designing reserves to conserve biodiversity that obviated the need for largely intuitive and highly problematic appeals to ecological theory at the time. But the scientific basis of these achievements and whether they constitute genuine scientific progress has been criticized. (...) We counter by pointing out important inaccuracies about the science and rejecting the apparent theory-first focus. More broadly, the case study reveals significant limitations of the predominant epistemic-semantic conceptions of scientific progress and the considerable merits of pragmatic, practically-oriented accounts. (shrink)

Aristotle is a political scientist and a student of biology. Political science, in his view, is concerned with the human good and thus it includes the study of ethics. He approaches many subjects from the perspective of both political science and biology: the virtues, the function of humans, and the political nature of humans. In light of the overlap between the two disciplines, I look at whether or not Aristotle’s views in biology influence or explain some of (...) his theses in political science. I show that we should not seek a unified answer to this question, for the relationship between the two disciplines varies depending on the topic. In some cases, e.g. the nature of the human function, the biological background is likely to be endorsed as one of the presuppositions of the ethical enquiry. In other cases, e.g. the study of social hierarchies, even though the ethical works and the biological works come to similar conclusions, it is hard to establish that the biological approach is intended to provide support to the ethico-political approach. In conclusion, I show that Aristotle’s political science and his biology are in conflict at least in two important cases: his account of justice towards non-human animals and his exhortation to contemplate. (shrink)

Open Science policies encourage researchers to disclose a wide range of outputs from their work, thus codifying openness as a specific set of research practices and guidelines that can be interpreted and applied consistently across disciplines and geographical settings. In this paper, we argue that this “one-size-fits-all” view of openness sidesteps key questions about the forms, implications, and goals of openness for research practice. We propose instead to interpret openness as a dynamic and highly situated mode of valuing (...) the research process and its outputs, which encompasses economic as well as scientific, cultural, political, ethical, and social considerations. This interpretation creates a critical space for moving beyond the economic definitions of value embedded in the contemporary biosciences landscape and Open Science policies, and examining the diversity of interests and commitments that affect research practices in the life sciences. To illustrate these claims, we use three case studies that highlight the challenges surrounding decisions about how––and how best––to make things open. These cases, drawn from ethnographic engagement with Open Science debates and semistructured interviews carried out with UK-based biologists and bioinformaticians between 2013 and 2014, show how the enactment of openness reveals judgments about what constitutes a legitimate intellectual contribution, for whom, and with what implications. (shrink)

Big data biology—bioinformatics, computational biology, systems biology (including ‘omics’), and synthetic biology—raises a number of issues for the philosophy of science. This article deals with several such: Is data-intensive biology a new kind of science, presumably post-reductionistic? To what extent is big data biology data-driven? Can data ‘speak for themselves?’ I discuss these issues by way of a reflection on Carl Woese’s worry that “a society that permits biology to become an engineering discipline, that allows that science (...) to slip into the role of changing the living world without trying to understand it, is a danger to itself.” And I argue that scientific perspectivism, a philosophical stance represented prominently by Giere, Van Fraassen, and Wimsatt, according to which science cannot as a matter of principle transcend our human perspective, provides the best resources currently at our disposal to tackle many of the philosophical issues implied in the modeling of complex, multilevel/multiscale phenomena. (shrink)

This book is a critical survey of and guidebook to the literature on biological functions. It ties in with current debates and developments, and at the same time, it looks back on the state of discourse in naturalized teleology prior to the 1970s. It also presents three significant new proposals. First, it describes the generalized selected effects theory, which is one version of the selected effects theory, maintaining that the function of a trait consists in the activity that led (...) to its differential persistence or reproduction in a population, and not merely its differential reproduction. Secondly, it advances “within-discipline pluralism” (as opposed to between-discipline pluralism) a new form of function pluralism, which emphasizes the coexistence of function concepts within diverse biological sub-disciplines. Lastly, it provides a critical assessment of recent alternatives to the selected effects theory of function, namely, the weak etiological theory and the systems-theoretic theory. The book argues that, to the extent that functions purport to offer causal explanations for the existence of a trait, there are no viable alternatives to the selected effects view. -/- The debate about biological functions is still as relevant and important to biology and philosophy as it ever was. Recent controversies surrounding the ENCODE Project Consortium in genetics, the nature of psychiatric classification, and the value of ecological restoration, all point to the continuing relevance to biology of philosophical discussion about the nature of functions. In philosophy, ongoing debates about the nature of biological information, intentionality, health and disease, mechanism, and even biological trait classification, are closely related to debates about biological functions. (shrink)

The integration of computer science, biology, and engineering has resulted in the emergence of rapidly growing interdisciplinary fields such as bioinformatics, bioengineering, DNA computing, and systems and synthetic biology. Ideas derived from computer science and engineering can provide innovative solutions to biological problems and advance research in new directions. Although interdisciplinary research has become increasingly prevalent in recent years, the scientists contributing to these efforts largely remain specialists in their original disciplines and are not fully capable (...) of covering the many facets of multidisciplinary problems, which impedes the development of truly integrated solutions. It would be .. (shrink)

Philosophy of biology is often said to have emerged in the last third of the twentieth century. Prior to this time, it has been alleged that the only authors who engaged philosophically with the life sciences were either logical empiricists who sought to impose the explanatory ideals of the physical sciences onto biology, or vitalists who invoked mystical agencies in an attempt to ward off the threat of physicochemical reduction. These schools paid little attention to actual biological science, (...) and as a result philosophy of biology languished in a state of futility for much of the twentieth century. The situation, we are told, only began to change in the late 1960s and early 1970s, when a new generation of researchers began to focus on problems internal to biology, leading to the consolidation of the discipline. In this paper we challenge this widely accepted narrative of the history of philosophy of biology. We do so by arguing that the most important tradition within early twentieth-century philosophy of biology was neither logical empiricism nor vitalism, but the organicist movement that flourished between the First and Second World Wars. We show that the organicist corpus is thematically and methodologically continuous with the contemporary literature in order to discredit the view that early work in the philosophy of biology was unproductive, and we emphasize the desirability of integrating the historical and contemporary conversations into a single, unified discourse. (shrink)

Scholars have paid great attention to the neo-Darwinism of Ronald Fisher. He was one of the founding fathers of the modern synthesis and, not surprisingly, his writings and life have been widely scrutinized. However, less attention has been paid to his interests in the human sciences. In assessing Fisher’s uses of the human sciences in his seminal book the Genetical Theory of Natural Selection and elsewhere, the article shows how Fisher’s evolutionary thought was essentially eclectic when applied to the human (...) context. In order to understand how evolution works among humans, Fisher made himself also a sociologist and historian. More than a eugenically minded Darwinist, Fisher was also a sophisticated scholar combining many disciplines without the ambition to reduce, simplistically, the human sciences to biology. (shrink)

The notion of science as a stratified system is clearly manifested in the markedly uneven distribution of productivity, rewards, resources, and recognition. Although previous studies have shown that institutional environments for conducting research differ significantly between national science systems, disciplines, and subfields, it remains to be shown whether any systematic variations and patterns in inequalities exist among researchers in different national and domain specific settings. This study investigates the positioning of citation elites as opposed to ‘ordinary’ researchers (...) by way of examining three dimensions of concentration (accumulation of publications and citations, specialisation, and institutional concentration) in biology, economics and physics in Denmark and the UK. Across all three dimensions, we put Richard Whitley’s bipartite theory to the test, suggesting a nexus between the intellectual structure of a discipline and the configuration of its elite. The study draws on a dataset of researchers who published most of their publications in either physics, biology, or economics over the 1980–2018 period and with at least one publication in 2017–2018 while affiliated to either a British or a Danish university. We find higher degrees of concentration in the UK compared to Denmark, and that physics and biology respectively display the greatest and lowest degree of concentration. Similar patterns in disciplinary differences are observed in both countries, suggesting that concentration patterns are largely rooted in disciplinary cultures and merely amplified by the national context. (shrink)

As biological and biomedical research increasingly reference the environmental context of the biological entities under study, the need for formalisation and standardisation of environment descriptors is growing. The Environment Ontology (ENVO) is a community-led, open project which seeks to provide an ontology for specifying a wide range of environments relevant to multiple life science disciplines and, through an open participation model, to accommodate the terminological requirements of all those needing to annotate data using ontology classes. This (...) paper summarises ENVO’s motivation, content, structure, adoption, and governance approach. (shrink)

Throughout art history, numerous artists have explored connections to science. In the society of today, the relationship between art and biology has been acquiring special visibility. Moreover, the current importance given to science and technology by today’s public opinion directly drives an increased awareness about the relationship between art and science. The public has been eagerly following breakthroughs in scientific research, albeit with mixed feelings: simultaneously awe, hope and fear for its potential misuse. Such awareness about (...) class='Hi'>biological sciences and biotechnology has been having an increasing influence over artists, where the artist is no longer a mere observer of the scientific research and not quite a science researcher, but rather an art researcher. This particular position has led to the development of strategies to promote the exploration of possibilities deriving from a cross-talk between artists and scientists. This is a new art practice, based on a ‘risk-based’ situation; a timeless research strategy to develop new methods of practice, new media and new ways to manipulate materials for artistic expression. This is art research. During the twentieth century, the key scientific advances – such as the discovery of the DNA structure, in vitro fertilization, transgenesis or the sequencing of the human genome (in the twenty-first century) – were perceived by society in diverse ways. The progressive incorporation of those concepts by society itself led to a point where biology and the medical sciences became the most promising areas of science. It is therefore not surprising that those same scientific disciplines have marked the development of the artistic discourse in a tremendous fashion, as well as also influencing all other areas of the contemporary society. Furthermore, these artworks explore new media, described as ‘moist’ in that they integrate dry in silico computer components with wet living biological systems. (shrink)

The writings of Joseph Henry Woodger (1894–1981) are often taken to exemplify everything that was wrongheaded, misguided, and just plain wrong with early twentieth-century philosophy of biology. Over the years, commentators have said of Woodger: (a) that he was a fervent logical empiricist who tried to impose the explanatory gold standards of physics onto biology, (b) that his philosophical work was completely disconnected from biological science, (c) that he possessed no scientific or philosophical credentials, and (d) that his (...) work was disparaged – if not altogether ignored – by the biologists and philosophers of his era. In this paper, we provide the first systematic examination of Woodger’s oeuvre, and use it to demonstrate that the four preceding claims are false. We argue that Woodger’s ideas have exerted an important influence on biology and philosophy, and submit that the current consensus on his legacy stems from a highly selective reading of his works. By rehabilitating Woodger, we hope to show that there is no good reason to continue to disregard the numerous contributions to the philosophy of biology produced in the decades prior to the professionalization of the discipline. (shrink)

Artists have always been known for pushing boundaries, or even refusing to accept that those boundaries exist in the first place. Contemporary academic structures and disciplinary boundaries evolved out of enlightenment thinking but were born as much from university administration systems, finance departments and evaluation systems that have no place in genuine knowledge creation or in our understanding of the world. Biology has inspired artists for centuries, but it is only in the last few decades that a new bioart movement (...) has emerged and artists have actively begun to collaborate with scientists to create works that use human and animal tissues, bacteria and living organisms as materials. In order to progress this important emerging field, we need to develop new frameworks that can help artists, cultural institutions, scientists and science institutions engage with and understand the various issues at play when making and exhibiting such work. The aim is to ultimately open up new avenues for participation and engagement from all elements of society. (shrink)

Mammalian synthetic biology holds the promise of providing novel therapeutic strategies, and the first success stories are beginning to be reported. Here we focus on the latest generation of mammalian transgene control devices, highlight state‐of‐the‐art synthetic gene network design, and cover prototype therapeutic circuits. These will have an impact on future gene‐ and cell‐based therapies and help bring drug discovery into a new era. The inventory of biological parts that are essential for life on this planet is becoming increasingly (...) complete. The postgenomic era has provided encyclopedic information on gene‐function correlations and systems biology is now delivering comprehensive details on the dynamics of biochemical reaction networks in living organisms. The time has come to reassemble these catalogued items and design new biological devices and systems with novel and useful functionality in a rational and systematic manner. This is the premise of synthetic biology, a constructive systems biology discipline likely to become the life science revolution of the 21st century. (shrink)

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

Science is a dynamic process in which the assimilation of new phenomena, perspectives, and hypotheses into the scientific corpus takes place slowly. The apparent disunity of the sciences is the unavoidable consequence of this gradual integration process. Some thinkers label this dynamical circumstance a ‘crisis’. However, a retrospective view of the practical results of the scientific enterprise and of science itself, grants us a clear view of the unity of the human knowledge seeking enterprise. This book provides many (...) arguments, case studies and examples in favor of the unity of science. These contributions touch upon various scientific perspectives and disciplines such as: Physics, Computer Science, Biology, Neuroscience, Cognitive Psychology, and Economics. (shrink)

‘‘Theoretical biology’’ is a surprisingly heter- ogeneous field, partly because it encompasses ‘‘doing the- ory’’ across disciplines as diverse as molecular biology, systematics, ecology, and evolutionary biology. Moreover, it is done in a stunning variety of different ways, using anything from formal analytical models to computer sim- ulations, from graphic representations to verbal arguments. In this essay I survey a number of aspects of what it means to do theoretical biology, and how they compare with the allegedly much more (...) restricted sense of theory in the physical sciences. I also tackle a recent trend toward the presentation of all-encompassing theories in the biological sciences, from general theories of ecology to a recent attempt to provide a conceptual framework for the entire set of biological disciplines. Finally, I discuss the roles played by philosophers of science in criticizing and shap- ing biological theorizing. (shrink)

The Latin conscius does not translate anything like mind or consciousness. Only in the mid-nineteenth century do we find the first attempts to study consciousness as its own discipline. Wundt, James, and Freud disagreed about how to approach the science of consciousness, although agreeing that psychology was a 'science of consciousness' that takes lived biological experience as its object. The behaviorists vetoed this idea. By the 1950s, for cognitive science, mind (conscious and unconscious) was considered analogous (...) to computer software. Recently, the science of consciousness has returned as Consciousness Studies, a new interdisciplinary synthesis of neuroscience, psychology, philosophy, and cultural anthropology. But what is new in this renaissance of the science of consciousness? New first, second and third person approaches all propose to take consciousness itself as a variable. This approach is as controversial as the nineteenth-century science of consciousness--controversy perhaps inherent to any science of consciousness. (shrink)

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

What does it mean to be a scientist working today; specifically, a scientist whose subject matter is human life? Scientists often overstate their claim to certainty, sorting the world into categorical distinctions that obstruct rather than clarify its complexities. In this book Daniel Nettle urges the reader to unpick such distinctions--biological versus social sciences, mind versus body, and nature versus nurture--and look instead for the for puzzles and anomalies, the points of connection and overlap. These essays, converted from often (...) humorous, sometimes autobiographical blog posts, form an extended meditation on the possibilities and frustrations of the life scientific. Pragmatically arguing from the intersection between social and biological sciences, Nettle reappraises the virtues of policy initiatives such as Universal Basic Income and income redistribution, highlighting the traps researchers and politicians are liable to encounter. This provocative, intelligent and self-critical volume is a testament to the possibilities of interdisciplinary study--whose virtues Nettle stridently defends--drawing from and having implications for a wide cross-section of academic inquiry. This will appeal to anybody curious about the implications of social and biological sciences for increasingly topical political concerns. It comes particularly recommended to Sciences and Social Sciences students and to scholars seeking to extend the scope of their field in collaboration with other disciplines. (shrink)

Reductionism--understanding complex processes by breaking them into simpler elements--dominates scientific thinking around the world and has certainly proved a powerful tool, leading to major discoveries in every field of science. But reductionism can be taken too far, especially in the life sciences, where sociobiological thinking has bordered on biological determinism. Thus popular science writers such as Richard Dawkins, author of the highly influential The Selfish Gene, can write that human beings are just "robot vehicles blindly programmed to (...) preserve the selfish molecules known as genes." Indeed, for many in science, genes have become the fundamental unit for understanding human existence: genes determine every aspect of our lives, from personal success to existential despair: genes for health and illness, genes for criminality, violence, and sexual orientation. Others would say that this is reductionism with a vengeance. In Lifelines, biologist Steven Rose offers a powerful alternative to the ultradarwinist claims of Dawkins, E.O. Wilson, Daniel Dennett and others. Rose argues against an extreme reductionist approach that would make the gene the key to understanding human nature, in favor of a more complex and richer vision of life. He urges instead that we focus on the organism and in particular on the organism's lifeline: the trajectory it takes through time and space. Our personal lifeline, Rose points out, is unique--even identical twins, with identical genes at birth, will differ over time. These differences are obviously not embedded in our genes, but come about through our developmental trajectory in which genes, as part of the biochemical orchestra of trillions of cells in each human body, have an important part--but only a part--to play. To illustrate this idea, Rose examines recent research in modern biology, and especially two disciplines--genetics (which looks at the impact of genes on form) and developmental biology (which examines the interaction between the organism and the environment)--and he explores new ideas on biological complexity proposed by scientists such as Stuart Kauffman. He shows how our lifelines are constructed through the interplay of physical forces--such as the intrinsic chemistry of lipids and proteins, and the self-organizing and stabilizing properties of complex metabolic webs--and he reaches a startling conclusion: that organisms are active players in their own fate, not simply the playthings of the gods, nature, or the inevitable workings out of gene-driven natural selection. The organism is both the weaver and the pattern it weaves. Lifelines will be a rallying point for all who seek an alternative to the currently fashionable, deeply determinist accounts which dominate popular science writing and, in fact, crowd the pages of some of the major scientific journals. Based on solid, state-of-the-art research, it not only makes important contributions to our understanding of Darwin and natural selection, but will swing the pendulum back to a richer, more complex view of human nature and of life. (shrink)