This chapter argues that scientific and philosophical progress in our understanding of the living world requires that we abandon a metaphysics of things in favour of one centred on processes. We identify three main empirical motivations for adopting a process ontology in biology: metabolic turnover, life cycles, and ecological interdependence. We show how taking a processual stance in the philosophy of biology enables us to ground existing critiques of essentialism, reductionism, and mechanicism, all of which have traditionally been (...) associated with substance ontology. We illustrate the consequences of embracing an ontology of processes in biology by considering some of its implications for physiology, genetics, evolution, and medicine. And we attempt to locate the subsequent chapters of the book in relation to the position we defend. (shrink)

Mayr’s proximate–ultimate distinction has received renewed interest in recent years. Here we discuss its role in arguments about the relevance of developmental to evolutionary biology. We show that two recent critiques of the proximate–ultimate distinction fail to explain why developmental processes in particular should be of interest to evolutionary biologists. We trace these failures to a common problem: both critiques take the proximate–ultimate distinction to neglect specific causal interactions in nature. We argue that this is implausible, and that the (...) distinction should instead be understood in the context of explanatory abstractions in complete causal models of evolutionary change. Once the debate is reframed in this way, the proximate–ultimate distinction’s role in arguments against the theoretical significance of evo-devo is seen to rely on a generally implicit premise: that the variation produced by development is abundant, small and undirected. We show that a “lean version” of the proximate–ultimate distinction can be maintained even when this isotropy assumption does not hold. Finally, we connect these considerations to biological practice. We show that the investigation of developmental constraints in evolutionary transitions has long relied on a methodology which foregrounds the explanatory role of developmental processes. It is, however, entirely compatible with the lean version of the proximate–ultimate distinction. (shrink)

Defending Robert Rosen’s claim that in every confrontation between physics and biology it is physics that has always had to give ground, it is shown that many of the most important advances in mathematics and physics over the last two centuries have followed from Schelling’s demand for a new physics that could make the emergence of life intelligible. Consequently, while reductionism prevails in biology, many biophysicists are resolutely anti-reductionist. This history is used to identify and defend a fragmented (...) but progressive tradition of anti-reductionist biomathematics. It is shown that the mathematicoephysico echemical morphology research program, the biosemiotics movement, and the relational biology of Rosen, although they have developed independently of each other, are built on and advance this antireductionist tradition of thought. It is suggested that understanding this history and its relationship to the broader history of post-Newtonian science could provide guidance for and justify both the integration of these strands and radically new work in post-reductionist biomathematics. (shrink)

I analyze the importance of parts in the style of biological theorizing that I call compositional biology. I do this by investigating various aspects, including partitioning frames and explanatory accounts, of the theoretical perspectives that fall under and are guided by compositional biology. I ground this general examination in a comparative analysis of three different disciplines with their associated compositional theoretical perspectives: comparative morphology, functional morphology, and developmental biology. I glean data for this analysis from canonical textbooks (...) and defend the use of such texts for the philosophy of science. I end with a discussion of the importance of recognizing formal and compositional biology as two genuinely different ways of doing biology – the differences arising more from their distinct methodologies than from scientific discipline included or natural domain studied. Ultimately, developing a translation manual between the two styles would be desirable as they currently are, at times, in conflict. (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)

Causal selection is the task of picking out, from a field of known causally relevant factors, some factors as elements of an explanation. The Causal Parity Thesis in the philosophy of biology challenges the usual ways of making such selections among different causes operating in a developing organism. The main target of this thesis is usually gene centrism, the doctrine that genes play some special role in ontogeny, which is often described in terms of information-bearing or programming. This paper (...) is concerned with the attempt of confronting the challenge coming from the Causal Parity Thesis by offering principles of causal selection that are spelled out in terms of an explicit philosophical account of causation, namely an interventionist account. I show that two such accounts that have been developed, although they contain important insights about causation in biology, nonetheless fail to provide an adequate reply to the Causal Parity challenge: Ken Waters's account of actual-difference making and Jim Woodward's account of causal specificity. A combination of the two also doesn't do the trick, nor does Laura Franklin-Hall's account of explanation (in this volume). We need additional conceptual resources. I argue that the resources we need consist in a special class of counterfactual conditionals, namely counterfactuals the antecedents of which describe biologically normal interventions. (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)

The idea behind this special theme journal issue was to continue the work we have started with the INBIOSA initiative (www.inbiosa.eu) and our small inter-disciplinary scientific community. The result of this EU funded project was a white paper (Simeonov et al., 2012a) defining a new direction for future research in theoretical biology we called Integral Biomathics and a volume (Simeonov et al., 2012b) with contributions from two workshops and our first international conference in this field in 2011. The initial (...) impulse for this effort was given a year earlier by a publication of one of the guest editors of this issue (Simeonov, 2010) in this journal. This time we wish to provide a broader forum and more space to elaborate in detail some of the most interesting concepts we have encountered in our discussions, as well as to invite some new contributions of particular interest in the field. Another goal we had in mind was to collect and review as many provocative perspectives as possible on the same key topic we are interested before making a decision to follow a more focused notion that would lead to a funded research program. Therefore we welcomed the generous suggestion of Professor Denis Noble, FRS, who is also editor of this journal to prepare a special theme issue entitled: “Can biology create a profoundly new mathematics and computation?” It has taken a while to invite and collect the contributions. Most of them had a couple of revision cycles and adjustments after having been thoroughly discussed with colleagues, incl. the editors of this issue. We think that the result we have obtained at the end is a satisfactory one, since we succeeded to integrate a diversity of original, but sometimes controversial and mutually excluding concepts organized within chapters of a self-contained volume. The task of compiling all this was not easy at all. Despite our efforts to position the articles of different authors and themes in a way allowing their easy comprehension and relation to each other within the individual chapters, some of them still require a sort of introduction to dissolve possible ambiguities. This is what we are going to do in the following few paragraphs with the hope that the reader (and some of the authors) would excuse our failures. (shrink)

A common view of how-possibly explanations in biology treats them as explanatorily incomplete. In addition to this interpretation of how-possibly explanation, I argue that there is another interpretation, one which features what I term “explanatory strategies.” This strategy-centered interpretation of how-possibly explanation centers on there being a different explanatory context within which how-possibly explanations are offered. I contend that, in conditions where this strategy context is recognized, how-possibly explanations can be understood as complete explanations. I defend this alternative interpretation (...) by analyzing the explanatory value of simple physical models the nineteenth century developmental biologist Wilhelm His constructed for animal development. (shrink)

Phylogeography, a relatively new subdicipline of evolutionary biology that attempts to unify the fields of phylogenetics and population biology in an explicit geographical context, has hosted in recent years a highly polarized debate related to the purported benefits and limitations that qualitative versus quantitative methods might contribute or impose on inferential processes in evolutionary biology. Here we present a friendly, non-technical introduction to the conflicting methods underlying the controversy, and exemplify it with a balanced selection of quotes (...) from the primary biological literature, to invite the philosophy of biology community to pay attention to the elements that have played a primary role in its presumed resolution. We also present the basic features of our own metascientific take on the debate, and point out—as a preliminary step in preparation for upcoming, more detailed treatments—the importance that appeals to authority in fields external to phylogeography per se have played in the current status of this highly visible evolutionary biology dispute. (shrink)

Among the many causes of an event, how do we distinguish the important ones? Are there ways to distinguish among causes on principled grounds that integrate both practical aims and objective knowledge? Psychologist Tania Lombrozo has suggested that causal explanations “identify factors that are ‘exportable’ in the sense that they are likely to subserve future prediction and intervention” (Lombrozo 2010, 327). Hence portable causes are more important precisely because they provide objective information to prediction and intervention as practical aims. However, (...) I argue that this is only part of the epistemology of causal selection. Recent work on portable causes has implicitly assumed them to be portable within the same causal system at a later time. As a result, it has appeared that the objective content of causal selection includes only facts about the causal structure of that single system. In contrast, I present a case study from systems biology in which scientists are searching for causal factors that are portable across rather than within causal systems. By paying careful attention to how these biologists find portable causes, I show that the objective content of causal selection can extend beyond the immediate systems of interest. In particular, knowledge of the evolutionary history of gene networks is necessary for correctly identifying causal patterns in these networks that explain cellular behavior in a portable way. (shrink)

Systems biologists often distance themselves from reductionist approaches and formulate their aim as understanding living systems “as a whole.” Yet, it is often unclear what kind of reductionism they have in mind, and in what sense their methodologies would offer a superior approach. To address these questions, we distinguish between two types of reductionism which we call “modular reductionism” and “bottom-up reductionism.” Much knowledge in molecular biology has been gained by decomposing living systems into functional modules or through detailed (...) studies of molecular processes. We ask whether systems biology provides novel ways to recompose these findings in the context of the system as a whole via computational simulations. As an example of computational integration of modules, we analyze the first whole-cell model of the bacterium M. genitalium. Secondly, we examine the attempt to recompose processes across different spatial scales via multi-scale cardiac models. Although these models rely on a number of idealizations and simplifying assumptions as well, we argue that they provide insight into the limitations of reductionist approaches. Whole-cell models can be used to discover properties arising at the interfaces of dynamically coupled processes within a biological system, thereby making more apparent what is lost through decomposition. Similarly, multi-scale modeling highlights the relevance of macroscale parameters and models and challenges the view that living systems can be understood “bottom-up.” Specifically, we point out that system-level properties constrain lower-scale processes. Thus, large-scale modeling reveals how living systems at the same time are more and less than the sum of the parts. (shrink)

Evolutionary developmental biology (Evo-Devo) is a new and rapidly developing field of biology which focuses on questions in the intersection of evolution and development and has been seen by many as a potential synthesis of these two fields. This synthesis is the topic of the books reviewed here. Integrating Evolution and Development (edited by Roger Sansom and Robert Brandon), is a collection of papers on conceptual issues in Evo-Devo, while From Embryology to Evo-Devo (edited by Manfred Laubichler and (...) Jane Maienschein) is a history of the problem of the relations between ontogeny and phylogeny. (shrink)

David Hull's analysis of conceptual change in science, as presentedin his book, Science as a Process (1988), provides a useful framework for understanding one of the scientific controversies in which he actively and constructively intervened, the units of selectiondebates in evolutionary biology. What follows is a brief overview ofthose debates and some reflections on them.

How does evolutionary biology fit with Thomas Kuhn's famous distinction between puzzle solving and paradigm shifts in science?

Philosophers have committed sins while studying science, it is said – philosophy of science focused on physics to the detriment of biology, reconstructed idealizations of scientific episodes rather than attending to historical details, and focused on theories and concepts to the detriment of experiments. Recent generations of philosophers of science have tried to atone for these sins, and by the 1980s the exculpation was in full swing. Marcel Weber’s Philosophy of Experimental Biology is a zenith mea culpa for (...) philosophy of science: it carefully describes several historical examples from twentieth century biology to address both ‘old’ philosophical topics, like reductionism, inference, and realism, and ‘new’ topics, like discovery, models, and norms. Biology, experiments, history – at last, philosophy of science, free of sin. (shrink)

Essentialism in philosophy is the position that things, especially kinds of things, have essences, or sets of properties, that all members of the kind must have, and the combination of which only members of the kind do, in fact, have. It is usually thought to derive from classical Greek philosophy and in particular from Aristotle’s notion of “what it is to be” something. In biology, it has been claimed that pre-evolutionary views of living kinds, or as they are sometimes (...) called, “natu-ral kinds”, are essentialist. This static view of living things presumes that no tran-sition is possible in time or form between kinds, and that variation is regarded as accidental or inessential noise rather than important information about taxa. In contrast it is held that Darwinian, and post-Darwinian, biology relies upon varia-tion as important and inevitable properties of taxa, and that taxa are not, therefore, kinds but historical individuals. Recent attempts have been made to undercut this account, and to reinstitute essentialism in biological kind terms. Others argue that essentialism has not ever been a historical reality in biology and its predecessors. In this chapter, I shall outline the many meanings of the notion of essentialism in psychology and social science as well as science, and discuss pro- and anti-essentialist views, and some recent historical revisionism. It turns out that nobody was essentialist to speak of in the sense that is antievolutionary in biology, and that much confusion rests on treating the one word, “essence” as meaning a single notion when in fact there are many. I shall also discuss the philosophical implica-tions of essentialism, and what that means one way or the other for evolutionary biology. Teaching about evolution relies upon narratives of change in the ways the living world is conceived by biologists. This is a core narrative issue. (shrink)

The scientific study of living organisms is permeated by machine and design metaphors. Genes are thought of as the ‘‘blueprint’’ of an organism, organisms are ‘‘reverse engineered’’ to discover their func- tionality, and living cells are compared to biochemical factories, complete with assembly lines, transport systems, messenger circuits, etc. Although the notion of design is indispensable to think about adapta- tions, and engineering analogies have considerable heuristic value (e.g., optimality assumptions), we argue they are limited in several important respects. In (...) particular, the analogy with human-made machines falters when we move down to the level of molecular biology and genetics. Living organisms are far more messy and less transparent than human-made machines. Notoriously, evolution is an oppor- tunistic tinkerer, blindly stumbling on ‘‘designs’’ that no sensible engineer would come up with. Despite impressive technological innovation, the prospect of artificially designing new life forms from scratch has proven more difficult than the superficial analogy with ‘‘programming’’ the right ‘‘software’’ would sug- gest. The idea of applying straightforward engineering approaches to living systems and their genomes— isolating functional components, designing new parts from scratch, recombining and assembling them into novel life forms—pushes the analogy with human artifacts beyond its limits. In the absence of a one-to-one correspondence between genotype and phenotype, there is no straightforward way to imple- ment novel biological functions and design new life forms. Both the developmental complexity of gene expression and the multifarious interactions of genes and environments are serious obstacles for ‘‘engi- neering’’ a particular phenotype. The problem of reverse-engineering a desired phenotype to its genetic ‘‘instructions’’ is probably intractable for any but the most simple phenotypes. Recent developments in the field of bio-engineering and synthetic biology reflect these limitations. Instead of genetically engi- neering a desired trait from scratch, as the machine/engineering metaphor promises, researchers are making greater strides by co-opting natural selection to ‘‘search’’ for a suitable genotype, or by borrowing and recombining genetic material from extant life forms. (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)

Symbiosis plays a fundamental role in contemporary biology, as well as in recent thinking in philosophy of biology. The discovery of the importance and universality of symbiotic associations has brought new light to old debates in the field, including issues about the concept of biological individuality. An important aspect of these debates has been the formulation of the hologenome concept of evolution, the notion that holobionts are units of natural selection in evolution. This review examines the philosophical assumptions (...) that underlie recent proposal of the hologenome concept of evolution, and traces those debates back in time to their historical origins, to the moment when the connection between the topics of symbiosis and biological individuality first caught the attention of biologists. The review is divided in two parts. The first part explores the historical origins of the connection between the notion of symbiosis and the concept of biological individuality, and emphasizes the role of A. de Bary, R. Pound, A. Schneider and C. Merezhkowsky in framing the debate. The second part examines the hologenome concept of evolution and explores four parallelisms between contemporary debates and the debates presented in the first part of the essay, arguing that the different debates raised by the hologenome concept were already present in the literature. I suggest that the novelty of the hologenome concept of evolution lies in the wider appreciation of the importance of symbiosis for maintaining life on Earth as we know it. Finally, I conclude by suggesting the importance of exploring the connections among contemporary biology, philosophy of biology and history of biology in order to gain a better understanding of contemporary biology. (shrink)

One of biology's fundamental aims is to generate understanding of the living world around—and within—us. In this chapter, I aim to provide a relatively nonpartisan discussion of the nature of explanation in biology, grounded in widely shared philosophical views about scientific explanation. But this discussion also reflects what I think is important for philosophers and biologists alike to appreciate about successful scientific explanations, so some points will be controversial, at least among philosophers. I make three main points: (1) (...) causal relationships and broad patterns have often been granted importance to scientific explanations, and they are in fact both important; (2) some explanations in biology cite the components of or processes in systems that account for the systems’ features, whereas other explanations feature large-scale or structural causes that influence a system; and (3) there can be multiple different explanations of a given biological phenomenon, explanations that respond to different research aims and can thus be compatible with one another even when they may seem to disagree. (shrink)

This collection of essays explores the metaphysical thesis that the living world is not made up of substantial particles or things, as has often been assumed, but is rather constituted by processes. The biological domain is organised as an interdependent hierarchy of processes, which are stabilised and actively maintained at different timescales. Even entities that intuitively appear to be paradigms of things, such as organisms, are actually better understood as processes. Unlike previous attempts to articulate processual views of biology, (...) which have tended to use Alfred North Whitehead’s panpsychist metaphysics as a foundation, this book takes a naturalistic approach to metaphysics. It submits that the main motivations for replacing an ontology of substances with one of processes are to be found in the empirical findings of science. Biology provides compelling reasons for thinking that the living realm is fundamentally dynamic, and that the existence of things is always conditional on the existence of processes. The phenomenon of life cries out for theories that prioritise processes over things, and it suggests that the central explanandum of biology is not change but rather stability, or more precisely, stability attained through constant change. This edited volume brings together philosophers of science and metaphysicians interested in exploring the consequences of a processual philosophy of biology. The contributors draw on an extremely wide range of biological case studies, and employ a process perspective to cast new light on a number of traditional philosophical problems, such as identity, persistence, and individuality. (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)

Despite numerous and increasing attempts to define what life is, there is no consensus on necessary and sufficient conditions for life. Accordingly, some scholars have questioned the value of definitions of life and encouraged scientists and philosophers alike to discard the project. As an alternative to this pessimistic conclusion, we argue that critically rethinking the nature and uses of definitions can provide new insights into the epistemic roles of definitions of life for different research practices. This paper examines the possible (...) contributions of definitions of life in scientific domains where such definitions are used most (e.g., Synthetic Biology, Origins of Life, Alife, and Astrobiology). Rather than as classificatory tools for demarcation of natural kinds, we highlight the pragmatic utility of what we call operational definitions that serve as theoretical and epistemic tools in scientific practice. In particular, we examine contexts where definitions integrate criteria for life into theoretical models that involve or enable observable operations. We show how these definitions of life play important roles in influencing research agendas and evaluating results, and we argue that to discard the project of defining life is neither sufficiently motivated, nor possible without dismissing important theoretical and practical research. (shrink)

Although it may seem like a truism to assert that biology is the science that studies organisms, during the second half of the twentieth century the organism category disappeared from biological theory. Over the past decade, however, biology has begun to witness the return of the organism as a fundamental explanatory concept. There are three major causes: (a) the realization that the Modern Synthesis does not provide a fully satisfactory understanding of evolution; (b) the growing awareness of the (...) limits of reductionism in molecular biology; and (c) the renewed interest in the nature of life as a genuine scientific problem. This essay examines these recent developments and considers the new epistemological roles being played by the organism in each of them. It also reflects on what the present resurgence of the organism means for the philosophy of biology. (shrink)

The scientific study of living organisms is permeated by machine and design metaphors. Genes are thought of as the ‘‘blueprint’’ of an organism, organisms are ‘‘reverse engineered’’ to discover their functionality, and living cells are compared to biochemical factories, complete with assembly lines, transport systems, messenger circuits, etc. Although the notion of design is indispensable to think about adaptations, and engineering analogies have considerable heuristic value (e.g., optimality assumptions), we argue they are limited in several important respects. In particular, the (...) analogy with human-made machines falters when we move down to the level of molecular biology and genetics. Living organisms are far more messy and less transparent than human-made machines. Notoriously, evolution is an opportunistic tinkerer, blindly stumbling on ‘‘designs’’ that no sensible engineer would come up with. Despite impressive technological innovation, the prospect of artificially designing new life forms from scratch has proven more difficult than the superficial analogy with ‘‘programming’’ the right ‘‘software’’ would suggest. The idea of applying straightforward engineering approaches to living systems and their genomes— isolating functional components, designing new parts from scratch, recombining and assembling them into novel life forms—pushes the analogy with human artifacts beyond its limits. In the absence of a one-to-one correspondence between genotype and phenotype, there is no straightforward way to implement novel biological functions and design new life forms. Both the developmental complexity of gene expression and the multifarious interactions of genes and environments are serious obstacles for ‘‘engineering’’ a particular phenotype. The problem of reverse-engineering a desired phenotype to its genetic ‘‘instructions’’ is probably intractable for any but the most simple phenotypes. Recent developments in the field of bio-engineering and synthetic biology reflect these limitations. Instead of genetically engineering a desired trait from scratch, as the machine/engineering metaphor promises, researchers are making greater strides by co-opting natural selection to ‘‘search’’ for a suitable genotype, or by borrowing and recombining genetic material from extant life forms. (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 semantic view of theories is normally considered to be an ac-count of theories congenial to Scientific Realism. Recently, it has been argued that Ontic Structural Realism could be fruitfully applied, in combination with the semantic view, to some of the philosophical issues peculiarly related to bi-ology. Given the central role that models have in the semantic view, and the relevance that mathematics has in the definition of the concept of model, the fo-cus will be on population genetics, which is (...) one of the most mathematized areas in biology. We will analyse some of the difficulties which arise when trying to use Ontic Structural Realism to account for evolutionary biology. (shrink)

The task of this essay is to put biological individuals in formal terms. This approach is not directly interested in matters of time (for example, in evolution), but rather in the formal shape of biological objects. So it is different from, but not opposed to, natural science. In his later years, Wittgenstein made similar investigations in psychology and mathematics. Unfortunately, he found no time to make extensive remarks on philosophy of biology. This is what we are going to advance (...) here. (shrink)

An influential position in the philosophy of biology claims that there are no biological laws, since any apparently biological generalization is either too accidental, fact-like or contingent to be named a law, or is simply reducible to physical laws that regulate electrical and chemical interactions taking place between merely physical systems. In the following I will stress a neglected aspect of the debate that emerges directly from the growing importance of mathematical models of biological phenomena. My main aim is (...) to defend, as well as reinforce, the view that there are indeed laws also in biology, and that their difference in stability, contingency or resilience with respect to physical laws is one of degrees, and not of kind . (shrink)

In this article, two different claims about nature are discussed. On the one hand, environmental philosophy has forced us to reflect on our position within nature. We are not the masters of nature as was claimed before. On the other hand there are the recent developments within synthetic biology. It claims that, now at last, we can be the masters of nature we have never been before. The question is then raised how these two claims must be related to (...) one another. Rather than stating that they are completely irreconcilable, I will argue for a dialogue aimed to discuss the differences and similarities. The claim is that we should not see it as two successive temporal phases of our relation to nature, but two tendencies that can coexist. (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)

The scientific status of evolutionary theory seems to be more or less perennially under question. I am not referring here (just) to the silliness of young Earth creation- ism (Pigliucci 2002; Boudry and Braeckman 2010), or even of the barely more intel- lectually sophisticated so-called Intelligent Design theory (Recker 2010; Brigandt this volume), but rather to discussions among scientists and philosophers of science concerning the epistemic status of evolutionary theory (Sober 2010). As we shall see in what follows, this debate (...) has a long history, dating all the way back to Darwin, and it is in great part rooted in the fundamental dichotomy between what French biologist and Nobel laureate Jacques Monod (1971) called chance and necessity—i.e., the inevitable and inextricable interplay of deterministic and stochastic mechanisms operating during the course of evolution. (shrink)

Although quantum mechanics can accurately predict the probability distribution of outcomes in an ensemble of identical systems, it cannot predict the result of an individual system. All the local and global hidden variable theories attempting to explain individual behavior have been proved invalid by experiments (violation of Bell’s inequality) and theory. As an alternative, Schrodinger and others have hypothesized existence of free will in every particle which causes randomness in individual results. However, these free will theories have failed to quantitatively (...) explain the quantum mechanical results. In this paper, we take the clue from quantum biology to get the explanation of quantum mechanical distribution. Recently it was reported that mutations (which are quantum processes) in DNA of E. coli bacteria instead of being random were biased in a direction such that the chance of survival of the bacteria is increased. Extrapolating it, we assume that all the particles including inanimate fundamental particles have a will and that is biased to satisfy the collective goals of the ensemble. Using this postulate, we mathematically derive the correct spin probability distribution without using quantum mechanical formalism (operators and Born’s rule) and exactly reproduce the quantum mechanical spin correlation in entangled pairs. Using our concept, we also mathematically derive the form of quantum mechanical wave function of free particle which is conventionally a postulate of quantum mechanics. Thus, we prove that the origin of quantum mechanical results lies in the will (or consciousness) of the objects biased by the collective goal of ensemble or universe. This biasing by the group on individuals can be called as “coherence” which directly represents the extent of life present in the ensemble. So, we can say that life originates out of establishment of coherence in a group of inanimate particles. (shrink)

Probably the most distinctive feature of synthetic biology is its being “synthetic” in some sense or another. For some, synthesis plays a unique role in the production of knowledge that is most distinct from that played by analysis: it is claimed to deliver knowledge that would otherwise not be attained. In this contribution, my aim is to explore how synthetic biology delivers knowledge via synthesis, and to assess the extent to which this knowledge is distinctly synthetic. On the (...) basis of distinctions between knowledge-how and knowledge-why, and between syntheses that succeed and syntheses that fail, I argue that the contribution of synthesis to knowledge is best understood when syntheses are construed as experimental interventions that aim at probing causal relationships between properties of the entities that are combined through these syntheses and properties of their target products. The distinctiveness of synthetic biology in its quest for knowledge through synthesis stems from its ability to sample at will a space of empirical possibilities that is not only huge but also that has been so scarcely sampled by nature. (shrink)

Synthetic biology is a field of research that concentrates on the design, construction, and modification of new biomolecular parts and metabolic pathways using engineering techniques and computational models. By employing knowledge of operational pathways from engineering and mathematics such as circuits, oscillators, and digital logic gates, it uses these to understand, model, rewire, and reprogram biological networks and modules. Standard biological parts with known functions are catalogued in a number of registries (e.g. Massachusetts Institute of Technology Registry of Standard (...) Biological Parts). Biological parts can then be selected from the catalogue and assembled in a variety of combinations to construct a system or pathway in a microbe. Through the innovative re-engineering of biological circuits and the optimization of certain metabolic pathways, biological modules can be designed to reprogram organisms to produce products or behaviors. Synthetic biology is what is known as a “platform technology”. That is, it generates highly transferrable theoretical models, engineering principles, and know-how that can be applied to create potential products in a wide variety of industries. Proponents suggest that applications of synthetic biology may be able to provide scientific and engineered solutions to a multitude of worldwide problems from health to energy. Synthetic biology research has already been successful in constructing microbial products which promise to offer cheaper pharmaceuticals such as the antimalarial synthetic drug artemisinin, engineered microbes capable of cleaning up oil spills, and the engineering of biosensors that can detect the presence of high concentrations of arsenic in drinking water. One of the potential benefits of synthetic biology research is in its application to biofuel production. It is this application which is the focus of this entry. The term “biofuel” has referred generally to all liquid fuels that are sourced from plant or plant byproducts and are used for energy necessary for transportation vehicles (Thompson 2012). Biofuels that are produced using synthetic biological techniques re-engineer microbes into biofuel factories are a subset of these. (shrink)

In our paper we investigate a difficulty arising when one tries to reconsiliateessentialis t’s thinking with classification practice in the biological sciences. The article outlinessome varieties of essentialism with particular attention to the version defended by Brian Ellis. Weunderline the basic difference: Ellis thinks that essentialism is not a viable position in biology dueto its incompatibility with biological typology and other essentialists think that these two elementscan be reconciled. However, both parties have in common metaphysical starting point and theylack (...) explicit track of methodological procedures. Methodological inquiry involves less demandingassumptions than metaphysical, and therefore it is justified to analyse abovementioned discrepancy between Ellis and other essentialist in this context. We do it by bottom-up investigation whichfocuses on the practice of taxonomists in the particular field of biology. A case study helps us todiscover four characteristics of biological typology practice: impossibility of algorithmization,relativity, subjectivity and conventionality. These features prove non-realistic and therefore anti-essentialistic character of biological classification. We conclude by saying that any essentialismrelated to the notion of biological kind cannot be regarded as justified by scientific enterprise of creating typologies. (shrink)

Unlike in physics, the category of thought experiment is not very common in biology. At least there are no classic examples that are as important and as well-known as the most famous thought experiments in physics, such as Galileo’s, Maxwell’s or Einstein’s. The reasons for this are far from obvious; maybe it has to do with the fact that modern biology for the most part sees itself as a thoroughly empirical discipline that engages either in real natural history (...) or in experimenting on real organisms rather than fictive ones. While theoretical biology does exist and is recognized as part of biology, its role within biology appears to be more marginal than the role of theoretical physics within physics. It could be that this marginality of theory also affects thought experiments as sources of theoretical knowledge. Of course, none of this provides a sufficient reason for thinking that thought experiments are really unimportant in biology. It is quite possible that the common perception of this matter is wrong and that there are important theoretical considerations in biology, past or present, that deserve the title of thought experiment just as much as the standard examples from physics. Some such considerations may even be widely known and considered to be important, but were not recognized as thought experiments. In fact, as we shall see, there are reasons for thinking that what is arguably the single most important biological work ever, Charles Darwin’s On the Origin of Species, contains a number of thought experiments. There are also more recent examples both in evolutionary and non-evolutionary biology, as we will show. Part of the problem in identifying positive examples in the history of biology is the lack of agreement as to what exactly a thought experiment is. Even worse, there may not be more than a family resemblance that unifies this epistemic category. We take it that classical thought experiments show the following characteristics: They serve directly or indirectly in the non-empirical epistemic evaluation of theoretical propositions, explanations or hypotheses. Thought experiments somehow appeal to the imagination. They involve hypothetical scenarios, which may or may not be fictive. In other words, thought experiments suppose that certain states of affairs hold and then try to intuit what would happen in a world where these suppositions are true. We want to examine in the following sections if there are episodes in the history of biology that satisfy these criteria. As we will show, there are a few episodes that might satisfy all three of these criteria, and many more if the imagination criterion is dropped or understood in a lose sense. In any case, this criterion is somewhat vague in the first place, unless a specific account of the imagination is presupposed. There will also be issues as to what exactly “non-empirical” means. In general, for the sake of discussion we propose to understand the term “thought experiment” here in a broad rather than a narrow sense here. We would rather be guilty of having too wide a conception of thought experiment than of missing a whole range of really interesting examples. (shrink)

The theory of evolution, which provides the conceptual framework for all modern research in organismal biology and informs research in molecular bi- ology, has gone through several stages of expansion and refinement. Darwin and Wallace (1858) of course proposed the original idea, centering on the twin concepts of natural selection and common descent. Shortly thereafter, Wallace and August Weismann worked toward the complete elimination of any Lamarckian vestiges from the theory, leaning in particular on Weismann’s (1893) concept of the (...) separation of soma and germ, resulting in what is some- times referred to as “neo-Darwinism”. (shrink)

What does it look like when a group of scientists set out to re-envision an entire field of biology in symbolic and formal terms? I analyze the founding and articulation of Numerical Taxonomy between 1950 and 1970, the period when it set out a radical new approach to classification and founded a tradition of mathematics in systematic biology. I argue that introducing mathematics in a comprehensive way also requires re-organizing the daily work of scientists in the field. Numerical (...) taxonomists sought to establish a mathematical method for classification that was universal to every type of organism, and I argue this intrinsically implicated them in a qualitative re-organization of the work of all systematists. I also discuss how Numerical Taxonomy’s re-organization of practice became entrenched across systematic biology even as opposing schools produced their own competing mathematical methods. In this way, the structure of the work process became more fundamental than the methodological theories that motivated it. (shrink)

The biological sciences have always proven a fertile ground for philosophical analysis, one from which has grown a rich tradition stemming from Aristotle and flowering with Darwin. And although contemporary philosophy is increasingly becoming conceptually entwined with the study of the empirical sciences with the data of the latter now being regularly utilised in the establishment and defence of the frameworks of the former, a practice especially prominent in the philosophy of physics, the development of that tradition hasn’t received the (...) wider attention it so thoroughly deserves. This review will briefly introduce some recent significant topics of debate within the philosophy of biology, focusing on those whose metaphysical themes (in everything from composition to causation) are likely to be of wide-reaching, cross-disciplinary interest. (shrink)

The aim of this paper is to describe and analyze the epistemological justification of a proposal initially made by the biomathematician Robert Rosen in 1958. In this theoretical proposal, Rosen suggests using the mathematical concept of “category” and the correlative concept of “natural equivalence” in mathematical modeling applied to living beings. Our questions are the following: According to Rosen, to what extent does the mathematical notion of category give access to more “natural” formalisms in the modeling of living beings? Is (...) the so -called “naturalness” of some kinds of equivalences (which the mathematical notion of category makes it possible to generalize and to put at the forefront) analogous to the naturalness of living systems? Rosen appears to answer “yes” and to ground this transfer of the concept of “natural equivalence” in biology on such an analogy. But this hypothesis, although fertile, remains debatable. Finally, this paper makes a brief account of the later evolution of Rosen’s arguments about this topic. In particular, it sheds light on the new role played by the notion of “category” in his more recent objections to the computational models that have pervaded almost every domain of biology since the 1990s. (shrink)

The cis-regulatory hypothesis is one of the most important claims of evolutionary developmental biology. In this paper I examine the theoretical argument for cis-regulatory evolution and its role within evolutionary theorizing. I show that, although the argument has some weaknesses, it acts as a useful example for the importance of current scientific debates for science education.

Review of Peter Godfrey-Smith's Philosophy of Biology.

Ideological language is widespread in theoretical biology. Evolutionary game theory has been defended as a worldview and a leap of faith, and sexual selection theory has been criticized for what it posits as basic to biological nature. Views such as these encourage the impression of ideological rifts in the field. I advocate an alternative interpretation, whereby many disagreements between different camps of biologists merely reflect methodological differences. This interpretation provides a more accurate and more optimistic account of the state (...) of play in the field of biology. It also helps account for biologists' tendency to embrace ideological positions. (shrink)

In her landmark book, Language, Thought, and Other Biological Categories (Millikan1984),1 Ruth Garrett Millikan utilizes the idea of a biological function to solve philosophical problems associated with the phenomena of language, thought, and meaning. Language and thought are activities of biological organisms, according to Millikan, and we should treat them as such when trying to answer related philosophical questions. Of special interest is Millikan’s treatment of intentionality. Here Millikan employs the notion of a biological function to explain what it is (...) for one thing in nature, a bee dance (43), for example, to be about another, in this case, the location of a nectar source. My concern in this paper is to understand whether Millikan’s account of intentionality adequately explains how humans achieve reference, in language or thought, to individuals and groups in their environment. In bringing her theory of intentional content to bear on human activities, Millikan focuses largely on natural language. Thus, in what follows, I begin by laying out the biology-based principles that underlie Millikan’s theory of content, then proceed with an explanation of how the theory is to apply to natural language. As it appears, Millikan’s account of how content is determined for natural language terms and sentences rests on the determinacy of intentional content at the psychological level. This leads me to take a careful look at what Millikan says about the content of mental representations, in hopes of finding a sufficient basis there for the application of Millikan’s theory of content to natural language. Ultimately, I conclude that Millikan’s theory faces a problem of vacuity. If we approach the theory as a theory of intentional content, intended to explain the nature of reference, the theory is lacking in an extremely important respect: Millikan explains how it could be one of the biological functions of a mental or natural language term to refer, without telling us precisely what in the natural order constitutes the reference relation.. (shrink)

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

Kant’s theory of biology in the Critique of the Power of Judgment may be rejected as obsolete and attacked from two opposite perspectives. In light of recent advances in biology one can claim contra Kant, on the one hand, that biological phenomena, which Kant held could only be explicated with the help of teleological principles, can in fact be explained in an entirely mechanical manner, or on the other, that despite the irreducibility of biology to physico-mechanical explanations, (...) it is nonetheless proper science. I argue in response that Kant’s analysis of organisms is by no means obsolete. It reveals biology’s uniqueness in much the same way as several current theorists do. It brings to the fore the unique purposive characteristics of living phenomena, which are encapsulated in Kant’s concept of “natural end” and which must be explicated in natural terms in order for biology to become a science. I maintain that Kant’s reluctance to consider biology proper science is not a consequence of his critical philosophy but rather of his inability to complete this task. Kant lacked an appropriate theoretical framework, such as provided later by modern biology, which would enable the integration of the unique features of biology in an empirical system. Nevertheless, as I show in this paper, the conceptual problems with which Kant struggled attest more to the relevance and depth of his insights than to the shortcomings of his view. His contribution to the biological thought consists in insisting on an empirical approach to biology and in providing the essential philosophical underpinning of the autonomous status of biology. (shrink)

Are living organisms--as Descartes argued--just machines? Or is the nature of life such that it can never be fully explained by mechanistic models? In this thought-provoking and controversial book, eminent geophysicist Walter M. Elsasser argues that the behavior of living organisms cannot be reduced to physico-chemical causality. Suggesting that molecular biology today is at the same point as Newtonian physics on the eve of the quantum revolution, Elsasser lays the foundation for a theoretical biology that points the way (...) toward a natural philosophy of organic life. Explicitly repudiating "vitalism" (the notion that the laws of nature need to be modified when applied to living organisms), Elsasser argues instead that the structural complexity of even a single living cell is "transcomputational"--that is, beyond the power of any imaginable system to compute. Beginning from this insight, Elsasser leads the reader through a step-by-step process that ultimately arrives at the conclusion that living and non-living matter are separated by "a no-man's land of irrationality." Trained in Germany as a physicist, Elsasser first pondered the implications of quantum mechanics for biology as early as 1951. The more closely he studied the inherent complexity of life, the more skeptical he became of the reductionist view of organisms as tiny machines. "An organism," he concluded, "is a source of causal chains which cannot be traced beyond a terminal point because they are lost in the unfathomable complexity of the organism." Like the physicist who works within the bounds of an unfathomable universe, Elsasser argues, the biologist must seek answers within a system that is no less unfathomable. (shrink)

In this paper I take evolutionary biology as an example to reflect on the role of philosophy and on the transformations that philosophy is constantly stimulated to do in its own approach when dealing with science. I consider that some intellectual movements within evolutionary biology (more specifically, the various calls for 'synthesis') express metascientific views, i.e., claims about 'what it is to do research' in evolutionary biology at different times. In the construction of metascientific views I see (...) a fundamental role to be played by philosophy, and, at the same time, a need to complement the philosophical methods with many more methods coming from other sciences. What leads philosophy out of itself is its own attention to scientific practice. My humble methodological suggestions are, at this stage, only meant to help us imagine metascientific views that are built with a more scientific, interdisciplinary approach, in order to attenuate partiality, subjectivity and impressionism in describing the scientific community. And yet, we should not be naïve and imbued with the myth of 'datadriven' research, especially in this field: other complex issues about metascientific views call for a serious, constant philosophical reflection on scientific practice. (shrink)