Biology is seen not merely as a privileged oppressor of women but as a co-victim of masculinist social assumptions. We see feminist critique as one of the normative controls that any scientist must perform whenever analyzing data, and we seek to demonstrate what has happened when this control has not been utilized. Narratives of fertilization and sex determination traditionally have been modeled on the cultural patterns of male/female interaction, leading to gender associations being placed on cells and their components. (...) We also find that when gender biases are controlled, new perceptions of these intracellular and extracellular relationships emerge. (shrink)

Perhaps because of it implications for our understanding of human nature, recent philosophy of biology has seen what might be the most dramatic work in the philosophies of the ”special” sciences. This drama has centered on evolutionary theory, and in the second edition of this textbook, Elliott Sober introduces the reader to the most important issues of these developments. With a rare combination of technical sophistication and clarity of expression, Sober engages both the higher level of theory and the (...) direct implications for such controversial issues as creationism, teleology, nature versus nurture, and sociobiology. Above all, the reader will gain from this book a firm grasp of the structure of evolutionary theory, the evidence for it, and the scope of its explanatory significance. (shrink)

This is a wide ranging and deeply learned examination of evolutionary developmental biology, and the foundations of life from the perspective of information theory. Hermeneutics was a method developed in the humanities to achieve understanding, in a given context, of texts, history, and artwork. In Readers of the Book of Life, the author shows that living beings are also hermeneutical interpreters of genetics texts saved in DNA; an interpretation based on the past experience of the cell (cell lineage, species), (...) confronted with and incorporating present environmental clues. This approach stresses the history, not only of the digital record saved in the DNA, but also of the flesh - the cellular organization which has a direct time-continuity with the very origins of life. This book is aimed at reconciling two opposite approaches to life. The first strictly sticking to a belief that all phenomena observed in the realm of the living can be explained from laws of physics. The opposite stressing the importance of features characteristic for a given level of description. To bring both views into a common understanding, the first part gives a comparison of the two problem solving strategies. The second part surveys the development of 20th century biology, bringing to light branches that never became part of the research mainstream. The third section of the book reviews a large body of recent evidence that can be interpreted in favor of the hermeneutic arguments. (shrink)

Drawing on work of the past decade, this volume brings together articles from the philosophy, history, and sociology of science, and many other branches of the biological sciences. The volume delves into the latest theoretical controversies as well as burning questions of contemporary social importance. The issues considered include the nature of evolutionary theory, biology and ethics, the challenge from religion, and the social implications of biology today (in particular the Human Genome Project).

The ultimate source of explanation in biology is the principle of natural selection. Natural selection means differential reproduction of genes and gene combinations. It is a mechanistic process which accounts for the existence in living organisms of end-directed structures and processes. It is argued that teleological explanations in biology are not only acceptable but indeed indispensable. There are at least three categories of biological phenomena where teleological explanations are appropriate.

This open access book assesses the prospects of (re)adopting organization as a pivotal concept in biology. It shows how organization can nourish biological thinking and practice, by reconnecting with the idea of biology as the science of organized systems. The book provides a comprehensive state-of-the-art picture of the characterizations and uses of the concept of organization in both biological science and philosophy of biology. It also deals with a variety of themes – including evolution, organogenesis, heredity, cognition (...) and ecology – with respect to which the concept of organization can guide the elaboration of original models and new experimental protocols. It will be of interest to biologists and scholars working in philosophy of science alike. (shrink)

This is an Element surveying the most important literature using game theory and evolutionary game theory to shed light on questions in the philosophy of biology. There are two branches of literature that the book focuses on. It begins with a short introduction to game theory and evolutionary game theory. It then turns to working using signaling games to explore questions related to communication, meaning, language, and reference. The second part of the book addresses prosociality - strategic behavior that (...) contributes to the successful functioning of social groups - using the prisoner's dilemma, stag hunt, and bargaining games. (shrink)

Synthetic biologists aim to generate biological organisms according to rational design principles. Their work may have many beneficial applications, but it also raises potentially serious ethical concerns. In this article, we consider what attention the discipline demands from bioethicists. We argue that the most important issue for ethicists to examine is the risk that knowledge from synthetic biology will be misused, for example, in biological terrorism or warfare. To adequately address this concern, bioethics will need to broaden its scope, (...) contemplating not just the means by which scientific knowledge is produced, but also what kinds of knowledge should be sought and disseminated. (shrink)

In addition to being one of the world's most influential philosophers, Aristotle can also be credited with the creation of both the science of biology and the philosophy of biology. He was the first thinker to treat the investigations of the living world as a distinct inquiry with its own special concepts and principles. This book focuses on a seminal event in the history of biology - Aristotle's delineation of a special branch of theoretical knowledge devoted to (...) the systematic investigation of animals. Aristotle approached the creation of zoology with the tools of subtle and systematic philosophies of nature and of science that were then carefully tailored to the investigation of animals. The papers collected in this volume, written by a pre-eminent figure in the field of Aristotle's philosophy and biology, examine Aristotle's approach to biological inquiry and explanation, his concepts of matter, form and kind, and his teleology. (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)

What is Life? This is the question asked by Denis Noble in this very personal and at times deeply lyrical book. Noble is a renowned physiologist and systems biologist, and he argues that the genome is not life itself: to understand what life is, we must view it at a variety of different levels, all interacting with each other in a complex web. It is that emergent web, full of feedback between levels, from the gene to the wider environment, that (...) is life. (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)

We argue for a conception of ‘philosophy of biology before biology’ which is neither internalist study of biological doctrines, nor a reconstruction of the role philosophical concepts might have played in the constitution of biology as science, but rather a kind of interplay between metaphysical and empirical issues. This should have an impact both on our present understanding of philosophy of biology, given that it is necessarily conditioned by a very specific history and historiography, and on (...) our understanding of how biology as a science of life became unified. (shrink)

The historical development of debates about reduction testifies to us that reductionism in biology must proceed by providing a precise and complete causal explanation for every biological phenomenon at the level of molecules. An intertheoretical reduction model was proposed in biology but proved unsuccessful due to its inability to accommodate and explain the success of molecular biology. Ever since the molecular structure of the gene was discovered, actual biological research has successfully generated explanations for complex biological facts (...) in terms of the predicates of molecular biology. Biological phenomena, which classical functional biology explains only with limited powers, are more accurately described and comprehensively explained as the reduction processes advance with molecular biology. It is clear that the reductionist research program of molecular biology is the best account of success and progress in biology. (shrink)

During the last twenty years, Kant's theory of biology has increasingly attracted the attention of scholars and developed into a field which is growing rapidly in importance within Kant studies. The volume presents fifteen interpretative essays written by experts working in the field, covering topics from seventeenth- and eighteenth-century biological theories, the development of the philosophy of biology in Kant's writings, the theory of organisms in Kant's Critique of the Power of Judgment, and current perspectives on the teleology (...) of nature. (shrink)

Ethical dilemmas raised by the use of nanotechnology in medical practice can be viewed from several perspectives: religious spiritualist perspective, the perspective of human dignity (nanotechnologies can be thought of as an affront to human dignity), the issue of controversial choice. The article aims to expose some bioethical dilemmas in using synthetic biology and nanotechnologies. Nowadays is often brought into discussion the fact it is possible to appear in the future new human species resulted not via natural selection and (...) evolution, but through the demiurgic effect of technology development in areas such as: synthetic biology, genetics, neurobiology and neurosciences, prosthesis technology and not least of artificial intelligence research. We will also refer into this paper at the possible raised challenges to ethicists who are oriented towards an ethics of species. Those challenges are raised right from the dawn of a consciousness of species, a social construction generated by changes of the meaning of belonging to humanity. During our article we argue that medical technology, especially genetics, medical assisted human reproduction and not least synthetic biology, require a rethinking ethical meanings of applying those technologies in everyday practices. (shrink)

Social scientific and humanistic research on synthetic biology has focused quite narrowly on questions of epistemology and ELSI. I suggest that to understand this discipline in its full scope, researchers must turn to the objects of the field—synthetic biological artifacts—and study them as the objects in the making of a science yet to be made. I consider one fundamentally important question: how should we understand the material products of synthetic biology? Practitioners in the field, employing a consistent technological (...) optic in the study and construction of biological systems, routinely employ the mantra ‘biology is technology’. I explore this categorization. By employing an established definition of technological artifects drawn from the philosophy of technology, I explore the appropriateness of attributing to synthetic biological artifacts the four criteria of materiality, intentional design, functionality, and normativity. I then explore a variety of accounts of natural kinds. I demonstrate that synthetic biological artifacts fit each kind imperfectly, and display a concomitant ontological ‘messiness’. I argue that this classificatory ambivalence is a product of the field’s own nascence, and posit that further work on kinds might help synthetic biology evaluate its existing commitments and practices. (shrink)

Synthetic biology is an umbrella term that covers a range of aims, approaches, and techniques. They are all brought together by common practices of analogizing, synthesizing, mechanicizing, and kludging. With a focus on kludging as the connection point between biology, engineering, and evolution, I show how synthetic biology’s successes depend on custom-built kludges and a creative, “make-it-work” attitude to the construction of biological systems. Such practices do not fit neatly, however, into synthetic biology’s celebration of rational (...) design. Nor do they straightforwardly embody Richard Feynman’s “last blackboard” statement that without creating something it cannot be understood. Reflecting further on the relationship between synthetic construction and knowledge making gives philosophy of science new avenues of insight into scientific practice. (shrink)

Symmetries play a major role in physics, in particular since the work by E. Noether and H. Weyl in the first half of last century. Herein, we briefly review their role by recalling how symmetry changes allow to conceptually move from classical to relativistic and quantum physics. We then introduce our ongoing theoretical analysis in biology and show that symmetries play a radically different role in this discipline, when compared to those in current physics. By this comparison, we stress (...) that symmetries must be understood in relation to conservation and stability properties, as represented in the theories. We posit that the dynamics of biological organisms, in their various levels of organization, are not just processes, but permanent (extended, in our terminology) critical transitions and, thus, symmetry changes. Within the limits of a relative structural stability (or interval of viability), variability is at the core of these transitions. (shrink)

Synthetic biology has a strong modal dimension that is part and parcel of its engineering agenda. In turning hypothetical biological designs into actual synthetic constructs, synthetic biologists reach towards potential biology instead of concentrating on naturally evolved organisms. We analyze synthetic biology’s goal of making biology easier to engineer through the combinatorial theory of possibility, which reduces possibility to combinations of individuals and their attributes in the actual world. While the last decades of synthetic biology (...) explorations have shown biology to be much more difficult to engineer than originally conceived, synthetic biology has not given up its combinatorial approach. (shrink)

A familiar position regarding the evolution of ethics is that biology can explain the origin of morals but that in doing so it removes the possibility of their having objective justification. This position is set fourth in detail in the writings of Michael Ruse but it is also taken by many others, notably, Jeffrie Murphy, Andrew Oldenquist, and Allan Gibbard, I argue the contrary view that biology provides a justification of the existence of morals which is objective in (...) the sense of being independent of people's moral views and their particular desires and preferences. Ironically, my argument builds on the very premises which are supposed to undermine the objectivity of morals. But my argument stops short of claiming that biology can give us a basis for justifying some particular system of morals. Drawing on an analogy with social contract theory, I offer a general reason why this more ambitious project cannot be expected to succeed if the argument is pursued along the same lines. Finally, I give reasons why the possibility of objective justification for a particular morality cannot be ruled out in general on evolutionary grounds. (shrink)

Knowledge of Life Today presents the thoughts of Jean Gayon, a major philosopher of science in France who is recognized across the Atlantic, especially for his work in philosophy and the history of life sciences. The book is structured around Gayon's personal answers to questions put forward by Victor Petit. This approach combines scientific rigor and risk-taking in answers that go back to the fundamentals of the subject. As well as the relationship between philosophy and the history of science, Gayon (...) discusses the main questions of the history and philosophy of biology that marked his intellectual journey: Darwin, evolutionary biology, genetics and molecular biology, human evolution, and various aspects of the relationship between biology and society in contemporary times (racism, eugenics, biotechnology, biomedicine, etc.). (shrink)

This major new series in the philosophy of science aims to provide a new generation of textbooks for the subject. The series will not only offer fresh treatments of core topics in the theory and methodology of scientific knowledge, but also introductions to newer areas of the discipline. Furthermore, the series will cover topics in current science that raise significant foundational issues both for scientific theory and for philosophy more generally. Biology raises distinct questions of its own not only (...) for philosophy of science, but for metaphysics, epistemology and ethics. This comprehensive new textbook for a rapidly growing field of study provides students new to the subject with an up-to-date presentation of the key philosophical issues. Care is taken throughout to keep the technicalities accessible to the non-biologist but without sacrificing the philosophical subtleties. The first part of the book covers the philosophical challenges posed by evolution and evolutionary biology, beginning with Darwin's central argument in the Origin of the Species. Individual chapters cover natural selection, the selfish gene, alternative units of selection, developmental systems theory, adaptionism and issues in macroevolution. The second part of the book examines philosophical questions arising in connection with biological traits, function, nature and nurture, and biological kinds. The third part of the book examines metaphysical questions, biology's relation with the traditional concerns of philosophy of science, and how evolution has been introduced into epistemological debates. The final part considers the relevance of biology to questions about ethics, religion and human nature. (shrink)

Synthetic biology is an increasingly high-profile area of research that can be understood as encompassing three broad approaches towards the synthesis of living systems: DNA-based device construction, genome-driven cell engineering and protocell creation. Each approach is characterized by different aims, methods and constructs, in addition to a range of positions on intellectual property and regulatory regimes. We identify subtle but important differences between the schools in relation to their treatments of genetic determinism, cellular context and complexity. These distinctions tie (...) into two broader issues that define synthetic biology: the relationships between biology and engineering, and between synthesis and analysis. These themes also illuminate synthetic biology's connections to genetic and other forms of biological engineering, as well as to systems biology. We suggest that all these knowledge-making distinctions in synthetic biology raise fundamental questions about the nature of biological investigation and its relationship to the construction of biological components and systems. (shrink)

Should the philosophy of biology deal with organismic, or with molecular aspects , or with both ? We are, of course, not the first to appreciate the ...

Due to the variation, contingency and complexity of living systems, biology is often taken to be a science without fundamental theories, laws or general principles. I revisit this question in light of the quest for design principles in systems biology and show that different views can be reconciled if we distinguish between different types of generality. The philosophical literature has primarily focused on generality of specific models or explanations, or on the heuristic role of abstraction. This paper takes (...) a different approach in emphasizing a theory-constituting role of general principles. Design principles signify general dependency-relations between structures and functions, given a set of formally defined constraints. I contend that design principles increase our understanding of living systems by relating specific models to general types. The categorization of types is based on a delineation of the scope of biological possibilities, which serves to identify and define the generic features of classes of systems. To characterize the basis for general principles through generic abstraction and reasoning about possibility spaces, I coin the term constraint-based generality. I show that constraint-based generality is distinct from other types of generality in biology, and argue that general principles play a unifying role that does not entail theory reduction. (shrink)

This paper examines the history of animal behavior studies after the synthesis period. Three episodes are considered: the adoption of the theory of natural selection, the mathematization of ideas, and the spread of molecular methods in behavior studies. In these three episodes, students of behavior adopted practices and standards developed in population ecology and population genetics. While they borrowed tools and methods from these fields, they made distinct uses that set them relatively apart and led them to contribute, in their (...) own way, to evolutionary theory. These episodes also highlight some limitations of “conjunction narratives” centered on the relation between a discipline and the modern synthesis. A trend in conjunction narratives is to interpret any development related to evolution in a discipline as an “extension,” an “integration,” or as a “delayed” synthesis. I here suggest that this can lead to underestimate discontinuities in the history of evolutionary biology. (shrink)

Concentrating on problems that commonly perplex general readers and beginning students, John Maynard Smith discusses fundamental issues in biology, with emphasis on evolution, development, and cognition. He provides a nontechnical account of molecular genetics, which is the foundation of modern biology, and explores such issues as heredity, animal behavior, the definition and origin of life, the brain and how we know things, artificial and natural intelligence, and genetics. The book is unique in presenting modern ideas in terms that (...) can be understood without an in-depth knowledge of biology. (shrink)

In this essay, I examine the controversy concerning the advocacy of ethical values in conservation biology. First, I argue, as others have, that conservation biology is a science laden with values both ethical and non-ethical. Second, after clarifying the notion of advocacy at work, I contend that conservation biologists should advocate the preservation of biological diversity. Third, I explore what ethical grounds should be used for advocating the preservation of ecological systems by conservation biologists. I argue that conservation (...) biologists should defend their preservationist positions on instrumentalist grounds alone if the context of discussion and debate is a scientific one. (shrink)

Evolutionary developmental biology (evo-devo) is considered a ‘mechanistic science,’ in that it causally explains morphological evolution in terms of changes in developmental mechanisms. Evo-devo is also an interdisciplinary and integrative approach, as its explanations use contributions from many fields and pertain to different levels of organismal organization. Philosophical accounts of mechanistic explanation are currently highly prominent, and have been particularly able to capture the integrative nature of multifield and multilevel explanations. However, I argue that evo-devo demonstrates the need for (...) a broadened philosophical conception of mechanisms and mechanistic explanation. Mechanistic explanation (in terms of the qualitative interactions of the structural parts of a whole) has been developed as an alternative to the traditional idea of explanation as derivation from laws or quantitative principles. Against the picture promoted by Carl Craver, that mathematical models describe but usually do not explain, my discussion of cases from the strand of evo-devo which is concerned with developmental processes points to qualitative phenomena where quantitative mathematical models are an indispensable part of the explanation. While philosophical accounts have focused on the actual organization and operation of mechanisms, properties of developmental mechanisms that are about how a mechanism reacts to modifications are of major evolutionary significance, including robustness, phenotypic plasticity, and modularity. A philosophical conception of mechanisms is needed that takes into account quantitative changes, transient entities and the generation of novel types of entities, feedback loops and complex interaction networks, emergent properties, and, in particular, functional-dynamical aspects of mechanisms, including functional (as opposed to structural) organization and distributed, system-wide phenomena. I conclude with general remarks on philosophical accounts of explanation. (shrink)

No single theory so far proposed gives a wholly satisfactory account of the origin and maintenance of bird-song dialects. This failure is the consequence of a weak comparative literature that precludes careful comparisons among species or studies, and of the complexity of the issues involved. Complexity arises because dialects seem to bear upon a wide range of features in the life history of bird species. We give an account of the principal issues in bird-song dialects: evolution of vocal learning, experimental (...) findings on song ontogeny, dialect descriptions, female and male reactions to differences in dialect, and population genetics and dispersal.We present a synthetic theory of the origin and maintenance of song dialects, one that accommodates most of the different systems reported in the literature. The few data available suggest that large, regional dialect populations are genetically differentiated; this pattern is correlated with reduced dispersal between dialects, assortative mating by females, and male-male exclusion. At the same time, “subdialects” may be formed within regional dialects. Subdialect clusters are usually small and may represent vocal mimicry among a few adjacent territorial males. The relative importance of genetic and social adaptation may contribute to the emergence of subdialects; their distinctiveness may be correlated with the degree of polygyny, for example. Thus, subdialect formation is linked to one theory of the evolution of repertoire size, but data are too fragmentary to examine this idea critically. (shrink)

Funding organizations around the world are adopting open science policies, resulting in a pressing need for open science programs. In response to the 2011 decadal survey, NASA sought to expand and accelerate omics research, releasing its GeneLab Strategic Plan in 2014. GeneLab is an open science data repository and analysis portal for spaceflight and space-relevant omics data. GeneLab’s output has been outstanding, but its full potential as a way to transform space biology has not yet been achieved. NASA should (...) pursue the development of GeneLab as an open science platorm in earnest. (shrink)

Evolutionary biology distinguishes differences in survival and reproduction rates due to selection from those due to drift. The distinction is usually thought to be founded in probabilistic facts: a difference in (say) two variants' average lifespans over some period of time that is due to selection is explained by differences in the probabilities relevant to survival; in the purest cases of drift, by contrast, the survival probabilities are equal and the difference in lifespans is a matter of chance. When (...) there is a difference in actual average lifespans there is always a difference in causal histories, but in drift, the causal differences make no contribution to the relevant probabilities. Some writers have claimed that the framework that determines which causes contribute to the probabilities, and so the framework that determines when the relevant probabilities differ and when they are equal, is imposed by modelers rather than being an objective fact of nature, and so that the distinction between selection and drift, however practically useful, is unreal. This paper uses my work on biological probabilities (Bigger than Chaos) and probabilistic explanation (Depth) to argue for the objectivity of, and the importance of the objectivity of, the distinction between selection and drift. (shrink)

This paper develops an account of explanation in biology which does not involve appeal to laws of nature, at least as traditionally conceived. Explanatory generalizations in biology must satisfy a requirement that I call invariance, but need not satisfy most of the other standard criteria for lawfulness. Once this point is recognized, there is little motivation for regarding such generalizations as laws of nature. Some of the differences between invariance and the related notions of stability and resiliency, due (...) respectively to Sandra Mitchell and Brian Skyrms, are explored. (shrink)

Theoretical biology and economics are remarkably similar in their reliance on mathematical models, which attempt to represent real world systems using many idealized assumptions. They are also similar in placing a great emphasis on derivational robustness of modeling results. Recently philosophers of biology and economics have argued that robustness analysis can be a method for confirmation of claims about causal mechanisms, despite the significant reliance of these models on patently false assumptions. We argue that the power of robustness (...) analysis has been greatly exaggerated. It is best regarded as a method of discovery rather than confirmation. (shrink)

In metaphysics and philosophy of science, a significant movement is making inroads, under the banner of ‘neo-Aristotelianism’. This movement has so far been focused primarily on the physical sciences; but given that Aristotle the natural scientist was above all a biologist, it is worth asking what a neo-Aristotelian philosophy of biology would look like? In this paper, I begin a discussion on precisely that question. One interesting result is that the fact that biology is now permeated by evolutionary (...) ways of thinking is all but irrelevant to answering that question. Far more important is how central are concepts of organic form, function and development to biology. Given recent developments, there are reasons to think at least some areas of the biological sciences would welcome a neo-Aristotelian philosophy of biology - i.e. a critical exploration of these concepts from an Aristotelian perspective. (shrink)

In this paper, I investigate the nature of a priori biological laws in connection with the idea that laws must be empirical. I argue that the epistemic functions of a priori biological laws in biology are the same as those of empirical laws in physics. Thus, the requirement that laws be empirical is idle in connection with how laws operate in science. This result presents a choice between sticking with an unmotivated philosophical requirement and taking the functional equivalence of (...) laws seriously and modifying our philosophical account. I favor the latter. (shrink)