Biology arises from the crowded molecular environment of the cell, rendering it a challenge to understand biological pathways based on the reductionist, low‐concentration in vitro conditions generally employed for mechanistic studies. Recent evidence suggests that low‐affinity interactions between cellular biopolymers abound, with still poorly defined effects on the complex interaction networks that lead to the emergent properties and plasticity of life. Mass‐action considerations are used here to underscore that the sheer number of weak interactions expected from the complex mixture (...) of cellular components significantly shapes biological pathway specificity. In particular, on‐pathway—i.e., “functional”—become those interactions thermodynamically and kinetically stable enough to survive the incessant onslaught of the many off‐pathway (“nonfunctional”) interactions. Consequently, to better understand the molecular biology of the cell a further paradigm shift is needed toward mechanistic experimental and computational approaches that probe intracellular diversity and complexity more directly. Also see the video abstract here https://youtu.be/T19X_zYaBzg. (shrink)

Universal ranks in folk biological taxonomy probably apply to taxonomies of cultural artifacts. We cannot call folk biological cognition domain-specific and modular. Color categorization may manifest unique organization, which would result from known neurology and the nature of color as an attribute. But folk biology does not adduce equivalent evidence. A global process of increasing differentiation similarly affects folk taxonomy, color categorization, and other practices germane to Atran's anthropology of science; this is beclouded by claims of specificity (...) and modularity. (shrink)

In recent years the notion of biological specificity has attracted significant philosophical attention. This paper focuses on host specificity, a kind of biological specificity that has not yet been discussed by philosophers, and which concerns the extent to which a species is selective in the range of other species it exploits for feeding and/or reproduction. Host specificity is an important notion in ecology, where it plays a variety of theoretical roles. Here I focus on (...) the role of host specificity in biological control, a field of applied ecology that deals with the suppression of pests through the use of living organisms. Examining host specificity and its role in biological control yields several valuable contributions to our understanding of biological specificity. In particular, I argue that host specificity cannot be fully understood in terms of Woodward’s well-known account of causal specificity. To adequately account for host specificity, we need a notion of causal specificity that takes into consideration the extent to which a variable’s effects are similar to one another – a dimension not captured in Woodward’s account. In addition, the literature on host specificity in biological control highlights certain aspects in which causally specific relationships can be practically valuable that have not yet been addressed in philosophical discussions of specificity. That literature also reveals that in certain contexts specificity can hinder rather than foster effective control, thus leading to a nuanced assessment of the practical value of specific causes. (shrink)

This paper attempts to elucidate three characteristics of causal relationships that are important in biological contexts. Stability has to do with whether a causal relationship continues to hold under changes in background conditions. Proportionality has to do with whether changes in the state of the cause “line up” in the right way with changes in the state of the effect and with whether the cause and effect are characterized in a way that contains irrelevant detail. Specificity is connected (...) both to David Lewis’ notion of “influence” and also with the extent to which a causal relation approximates to the ideal of one cause–one effect. Interrelations among these notions and their possible biological significance are also discussed. (shrink)

The assumption of domain specificity has been invaluable to the study of the emergence of biological thought in young children. Yet, domains of thought must be understood within a broader context that explains how those domains relate to the surrounding cultures, to different kinds of cognitive constraints, to framing effects, to abilities to evaluate knowledge and to the ways in which domain-specific knowledge in any individual mind is related to knowledge in other minds. All of these issues must (...) come together to have a full account of conceptual development in biology. (shrink)

Several authors have used the notion of causal specificity in order to defend non-parity about genetic causes (Waters 2007, Woodward 2010, Weber 2017, forthcoming). Non-parity in this context is the idea that DNA and some other biomolecules that are often described as information-bearers by biologists play a unique role in life processes, an idea that has been challenged by Developmental Systems Theory (e.g., Oyama 2000). Indeed, it has proven to be quite difficult to state clearly what the alleged special (...) role of genetic causes consists in. In this paper, I show that the set of biomolecules that are normally considered to be information-bearers (DNA, mRNA) can be shown to be the most specific causes of protein primary structure, provided that causal specificity is measured over a relevant space of biological possibilities, disregarding physical as well as logically possible states of the causal variables. (shrink)

Griffiths et al. (2015) have proposed a quantitative measure of causal specificity and used it to assess various attempts to single out genetic causes as being causally more specific than other cellular mechanisms, for example, alternative splicing. Focusing in particular on developmental processes, they have identified a number of important challenges for this project. In this discussion note, I would like to show how these challenges can be met.

Dr. Northoff's comprehensive comparison of clinical symptoms and neurobiological findings in catatonia with that of Parkinson's disease through integration of various levels of investigation, from neurochemistry up to the subjective experience, is a good example of the new strategies we need to improve our understanding of psychiatric disorders. His multimodal approach, leading to the hypothesis that different pathophysiologies of transcortical “horizontal modulation” and “bottom-up/top-down” – orbitofrontal/basal ganglia – “vertical modulations,” may explain many clinical aspects of catatonia and Parkinson's disease, and (...) thereby fills an important gap in current theories of psychomotor syndromes. However, to analyze more specifically the pathophysiology of catatonia, comparison not only with Parkinson's disease, but also with schizophrenia and anxiety disorders would be helpful. As long as the pathohistological and molecular basis of catatonic syndromes is unknown, theories based mainly on functional considerations remain preliminary. (shrink)

A common reductionist assumption is that macro-scale behaviors can be described "bottom-up" if only sufficient details about lower-scale processes are available. The view that an "ideal" or "fundamental" physics would be sufficient to explain all macro-scale phenomena has been met with criticism from philosophers of biology. Specifically, scholars have pointed to the impossibility of deducing biological explanations from physical ones, and to the irreducible nature of distinctively biological processes such as gene regulation and evolution. This paper takes a (...) step back in asking whether bottom-up modeling is feasible even when modeling simple physical systems across scales. By comparing examples of multi-scale modeling in physics and biology, we argue that the “tyranny of scales” problem presents a challenge to reductive explanations in both physics and biology. The problem refers to the scale-dependency of physical and biological behaviors that forces researchers to combine different models relying on different scale-specific mathematical strategies and boundary conditions. Analyzing the ways in which different models are combined in multi-scale modeling also has implications for the relation between physics and biology. Contrary to the assumption that physical science approaches provide reductive explanations in biology, we exemplify how inputs from physics often reveal the importance of macro-scale models and explanations. We illustrate this through an examination of the role of biomechanics modeling in developmental biology. In such contexts, the relation between models at different scales and from different disciplines is neither reductive nor completely autonomous, but interdependent. (shrink)

The concept of causal specificity is drawing considerable attention from philosophers of biology. It became the rationale for rejecting (and occasionally, accepting) a thesis of causal parity of developmental factors. This literature assumes that attributing specificity to causal relations is at least in principle a straightforward (if not systematic) task. However, the parity debate in philosophy of biology seems to be stuck at a point where it is not the biological details that will help move forward. In (...) this paper, I take a step back to reexamine the very idea of causal specificity and its intended role in the parity dispute in philosophy of biology. I contend that the idea of causal specificity across variations as currently discussed in the literature is irreducibly twofold in nature: it is about two independent components that are not mutually entailed. I show this to be the source of prior complications with the notion of specificity itself that ultimately affect the purposes for which it is often invoked, notably to settle the parity dispute. (shrink)

Atran adds a synthesis of much of the literature on folk-biological classification to important new experimental data relevant to long-standing inferences about the structure of folk taxonomies. What we know about such systems is somewhat overstated, and key issues remain unresolved, especially concerning the centrality of “generic species,” the primacy of “general purpose” taxonomies, and domain specificity.

Understanding biological systems in terms of scientific materialism has arguably reached a frontier, leaving fundamental questions about their complexity unanswered. In 1998, Friedrich Cramer proposed a general resonance theory as a way forward. His theory builds on the extension of the quantum physical duality of matter and wave to the macroscopic world. According to Cramer’ theory, agents constituting biological systems oscillate, akin to musical soundwaves, at specific eigenfrequencies. Biological system dynamics can be described as “Symphonies of Life” (...) emerging from the resonance (and dissonance) of eigenfrequencies within the interacting collective. His theory has potential for studying biological problems of increasing complexity in a fast‐changing Anthropocene from a new and transdisciplinary angle. Despite data becoming increasingly available for analyses, Cramer's theory remains ignored and therefore untested a quarter century after its publication. This paper discusses how the theory can move to quantitative assessments and application. Cramer's general resonance theory deserves revival. (shrink)

From its first proposal, the Central Dogma had a graphical form, complete with arrows of different types, and this form quickly became its standard presentation. In different scientific contexts, arrows have different meanings and in this particular case the arrows indicated the flow of information among different macromolecules. A deeper analysis illustrates that the arrows also imply a causal statement, directly connected to the causal role of genetic information. The author suggests a distinction between two different kinds of causal links, (...) defined as 'physical causality' and 'biological determination', both implied in the production of biological specificity. (shrink)

Adults have been shown to attribute certain properties more frequently than others to the dead. This category-specific pattern has been interpreted in terms of simulation constraints, whereby it may be harder to imagine the absence of some states than others. Afterlife beliefs have also shown context-sensitivity, suggesting that environmental exposure to different types of information might influence adults? reasoning about post-death states. We sought to clarify category and context effects in adults afterlife reasoning. Participants read a story describing the death (...) of a human protagonist after exposure to a biological prime, an emotional prime, or no prime. Emotions, desires, and epistemic states were more frequently attributed to the dead character than biological, psychobiological, and perceptual states, partially replicating previous findings. The biological prime decreased the attribution of certain post-death states relative to the control condition, whereas the emotional prime had no effect. Simulation theory does not provide a satisfactory explanation of the present findings, which may be better accounted for by conflict between different cognitive systems that are engaged in thinking about the dead. (shrink)

Different cell lineages growing in microgravity undergo a spontaneous transition leading to the emergence of two distinct phenotypes. By returning these populations in a normal gravitational field, the two phenotypes collapse, recovering their original configuration. In this review, we hypothesize that, once the gravitational constraint is removed, the system freely explores its phenotypic space, while, when in a gravitational field, cells are “constrained” to adopt only one favored configuration. We suggest that the genome allows for a wide range of “possibilities” (...) but it is unable per se to choose among them: the emergence of a specific phenotype is enabled by physical constraints that drive the system toward a preferred solution. These findings may help in understanding how cells and tissues behave in both development and cancer. In microgravity, cells undergo spontaneous and reversible transitions between different phenotypes. In the absence of physical constraints, living systems could yield bi-stable decisions. On the contrary, physical ‘boundaries’ constrain cells to acquire only a specific configuration by selecting and shaping different gene expression patterns provided by the intrinsic genetic stochasticity. (shrink)

Biomedicine is typically defined as the branch of medicine that is based on the principles of biology and biochemistry. A central tenet for biomedicine is the notion of disease and therapeutic specificity, i.e. the idea of tailored treatments for discrete disorders underpinned by specific pathologies. The present paper is concerned with how notions of disease and therapeutic specificity guide biomedical reasoning. To that end, the author proposes a model – the specificity triad – that draws on late (...) philosopher and physician Ludwik Fleck’s concept of “style of thought” to offer a frame for investigating the intricate process through which links between disorders, mechanisms, and therapeutics are established by biomedicine. Next by applying the specificity triad model to scrutinize research efforts in two discrete areas of medicine—psychiatry and regenerative medicine—this paper seeks to stimulate pertinent discussions in and about biomedicine. These include discussions on the ambiguous epistemic status of psychiatry within contemporary biomedicine, as well as the relationship between developmental biology — historically relatively disjointed from biomedical enterprise — and the burgeoning field of regenerative medicine. (shrink)

Previous work has suggested that many stem cells can be found in microanatomic niches, where adjacent somatic cells of the niche control the differentiation and proliferation states of their resident stem cells. Recently published work examining intestinal stem cells (ISCs) in the adult Drosophila midgut suggests a new paradigm where some stem cells actively control the cell fate decisions of their daughters. Here, we review recent literature(1) demonstrating that, in the absence of a detectable stem cell niche, multipotent Drosophila ISCs (...) modulate the Notch signaling pathway in their adjacent daughter cells in order to specify the differentiated lineages of their descendants. These observations made in Drosophila are challenging and advancing our understanding of stem cell biology. BioEssays 30:107–109, 2008. © 2008 Wiley Periodicals, Inc. (shrink)

Frequent evolutionary birth and death events have created a large quantity of biologically important, lineage‐specific DNA within mammalian genomes. The birth and death of DNA sequences is so frequent that the total number of these insertions and deletions in the human population remains unknown, although there are differences between these groups, e.g. transposable elements contribute predominantly to sequence insertion. Functional turnover – where the activity of a locus is specific to one lineage, but the underlying DNA remains conserved – can (...) also drive birth and death. However, this does not appear to be a major driver of divergent transcriptional regulation. Both sequence and functional turnover have contributed to the birth and death of thousands of functional promoters in the human and mouse genomes. These findings reveal the pervasive nature of evolutionary birth and death and suggest that lineage‐specific regions may play an important but previously underappreciated role in human biology and disease. (shrink)

It is widely assumed that selection history accounts of function can support a fully reductive naturalization of functional properties. I argue that this assumption is false. A problem with the alternative causal role account of function in this context is that it invokes the teleological notion of a goal in analysing real function. The selection history account, if it is to have reductive status, must not do the same. But attention to certain cases of selection history in biology, specifically those (...) involving meiotic drive, shows that selection historical explanations are available in the case of items without any plausible function. Making contributions to goals, here fitness, must be introduced as an additional constraint in the analysis, either explicitly, or implicitly by appeal to individual functions or the selection-of/selection-for distinction. (shrink)

This article examines how minimal genome research mobilizes philosophical concepts such as minimality and essentiality. Following a historical approach the article aims to uncover what function this terminology plays and which problems are raised by them. Specifically, four historical moments are examined, linked to the work of Harold J. Morowitz, Mitsuhiro Itaya, Eugene Koonin and Arcady Mushegian, and J. Craig Venter. What this survey shows is a historical shift away from historical questions about life or descriptive questions about specific organisms (...) towards questions that explore biological possibilities: what are possible forms of minimal genomes, regardless of whether they exist in nature? Moreover, it highlights a fundamental ambiguity at work in minimal genome research between a universality claim and a standardization claim: does a minimal genome refer to the minimal gene set for any organism whatsoever? Or does it refer rather to a gene set that will provide stable, robust and predictable behaviour, suited for biotechnological applications? Two diagnoses are proposed for this ambiguity: a philosophical diagnosis of how minimal genome research either misunderstands the ontology of biological entities or philosophically misarticulates scientific practice. Secondly, a historical diagnosis that suggests that this ambiguity is part of a broader shift towards technoscience. (shrink)

Griffiths et al. have proposed a quantitative measure of causal specificity and used it to assess various attempts to single out genetic causes as being causally more specific than other cellular mechanisms, for example, alternative splicing. Focusing in particular on developmental processes, they have identified a number of important challenges for this project. In this discussion note, I would like to show how these challenges can be met.

A specific mapping mechanism is defined as the basic unit of “Biological Memory”. This mechanism must account for the characteristic frequency patterns in the organic world, where future probability is a function of past experience. The conditions for the function of biological memory are analysed. It is found that asymmetry, and irreversibility as a consequence of complexity, are the basic principles of memory function. The essential asymmetries in genetic memory are pointed out, and the problem of bilateral symmetry (...) in a basically asymmetrical organization is briefly outlined.Complexity is defined in terms of symmetry. The thermodynamic arrow of time and the biological arrow of time are discussed in relation to elementarity and complexity with their specific types of repeatabilities: non-accumulative in the first case and accumulative as a result of “copy-reproduction” by memory in the second case. The application of terminology from Information Theory and Thermodynamics to Memory Mechanics is critically considered.The immediate and inevitable consequences of memory function are shown to be irreversible expansion and irreversible, unpredictable diversification, leading to growing complexity and size on all but the sub-molecular levels of biological structure. (shrink)

In presenting this paper for the Festschrift in honor of my long time friend, Charles Hartshorne, I should state at once that I am writing as a biologist, specifically a geneticist, interested in the philosophical implications of his subject, but with only a superficial knowledge of philosophy in general. My justification for writing on this topic is the belief that the philosophy of science is necessarily a joint venture since it is obvious that advances in science provide data on the (...) nature of existence which must be taken into account in philosophical consideration of this subject. This is most obvious in connection with the drastic revision of the basic concepts of physics since 1900, the impact of which on philosophy has recently been brilliantly developed by Čapek. There have also been great advances in biology. The resulting concepts do not strike at the very categories of thought and defy expression in language as do those of modern physics. Nevertheless they have a special importance from the facts that the only direct knowledge of mind that any one possesses is associated with a certain living organism, himself, and that in general, indications of the presence of mind are restricted to living organisms. The fact that while such indications are universally accepted in the case of other human beings but become progressively less convincing as we pass to animals closely similar to man, and from these to such forms as fishes, insects, clams, worms and protozoa, raises difficulties. Few see any indication of mind in plants. (shrink)

In lieu of an abstract, here is a brief excerpt of the content:Reviewed by:Nietzsche, Biology and MetaphorBabette E. BabichGregory Moore. Nietzsche, Biology and Metaphor. New York: Cambridge University Press, 2002. Pp. viii + 228. Cloth, $55.00.Gregory Moore's Nietzsche, Biology and Metaphor is a well-written book on a topic of growing importance in Nietzsche studies. Not only concerned with offering an interpretation of Nietzsche in terms of biology and metaphor, Moore's approach offers a literary contextualization of Darwinism in the history of (...) ideas but also in terms of an important reflection on the idea of decadence so important to Nietzsche and so influential in theorizing public health and law in the twentieth century, most perniciously in its deadly expressions in Nazi propaganda. Moore is thus able to bridge the fields of the more specifically linguistic study of metaphor and source-scholarship. To Moore's great credit, he seeks to emphasize the extent to which Nietzsche's thought was developed in active correspondence with the scientific literature and debates of his age. But this reviewer thinks it important to warn those with classical or traditional interest in metaphor that the text presupposes that the reader (and this is also to say that Moore) knows a Nietzschean metaphor when he sees one.Moore begins with the question of Nietzsche's Darwinism, focusing on the physiology of power to explore the relations between Darwin, Spencer, Lamarck, and Rolph, but also Nietzsche's favorites, Malthus and Lange, etc. The discussion of the history of the reception of Darwin's ideas is careful and extensive and offers an insightful clarification of Darwin (necessary to distinguish Darwin from Darwinism, "social" and otherwise). Some readers will find it even more Anglophone than seems justified by Darwin's heritage, despite Moore's passing references to Cuvier and (at rather greater length) Haeckel and Roux.This reviewer notes that the latter references have been well-discussed in the German literature and to some great part Moore is fair to this tradition even if it is also true that the discussion never enters the level of the history of science as this reader, for one, might have wished. In the case of Moore's interpretation of Nietzsche's texts, the readings sometimes suggest a reprise of what has come to be the consensus (and not just among Nietzsche scholars) of views on Nietzsche's thinking. Thus where certain secondary authors are in force in Moore's well-documented account (Pick, Moles, and Ruse), others are missing. Indeed, in the case of Nietzsche and Darwinism, Frederick Gregory's Nature Lost? Natural Science and the German Theological Traditions of the Nineteenth Century (Cambridge, 1992) offers an important supplement. Another book that seems to have been overlooked is Timothy Lenoir, The Strategy of Life: Teleology and Mechanics in Nineteenth Century German Biology (Dordrecht, 1982), and those interested in von Baer and other proponents of teleology in biology will find Lenoir's broader account useful.The second half of the book addresses degeneration and like most contemporary discussions, Moore's book is charged with the political history of the last century. Moore reviews the association of decadence with jazz music and—via physiognomy as its external signifier—to the ugly, the Jew, the Black, and, of course, to women who broke with the family role. As an instantiation, Moore uncovers the nineteenth century antipathy to "allegedly aberrant behavior such as masturbation and homosexuality" in Nietzsche's "restrictive" [End Page 348] (133) view of sexuality and precocious eroticism (134) as degeneration. However, the issue of masturbation is complicated. The nineteenth-century perspective on masturbation was less a matter of prudishness than a judgment backed with considerable social and medical force, which equated the practice with sickness or criminality, the counterpart to which today would be our judgment with regard to an addiction to cocaine or heroine. This censure drove Wagner's "exposure" of Nietzsche's personal dependence on this practice. Readers interested in this question can either take themselves to the easy-to-find because eponymous chapter in Marc Wiener's Richard Wagner and the Anti-Semitic Imagination (Lincoln, 1995) or to David B. Allison's account of this as the occasion for the break between Nietzsche and Wagner in Reading... (shrink)

In this paper I analyze the process by which modelers in systems biology arrive at an adequate representation of the biological structures thought to underlie data gathered from high-throughput experiments. Contrary to views that causal claims and explanations are rare in systems biology, I argue that in many studies of gene regulatory networks modelers aim at a representation of causal structure. In addressing modeling challenges, they draw on assumptions informed by theory and pragmatic considerations in a manner that is (...) guided by an interventionist conception of causal structure. While doubts have been raised about the applicability of this notion of causality to complex biological systems, it is here seen to be an adequate guide to inquiry. (shrink)

Systems biology is today such a widespread discipline that it becomes difficult to propose a clear definition of what it really is. For some, it remains restricted to the genomic field. For many, it designates the integrated approach or the corpus of computational methods employed to handle the vast amount of biological or medical data and investigate the complexity of the living. Although defining systems biology might be difficult, on the other hand its purpose is clear: systems biology, with (...) its emerging subfields systems medicine and systems pharmacology, clearly aims at making sense of complex observations/experimental and clinical datasets to improve our understanding of diseases and their treatments without putting aside the context in which they appear and develop. In this short review, we aim to specifically focus on these new subfields with the new theoretical tools and approaches that were developed in the context of cancer. Systems pharmacology and medicine now give hope for major improvements in cancer therapy, making personalized medicine closer to reality. As we will see, the current challenge is to be able to improve the clinical practice according to the paradigm shift of systems sciences. (shrink)

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

Several attempts have been made previously to provide a biological grounding for cognitive architectures by relating their components to the computations of specific brain circuits. Often, the architecture's action selection system is identified with the basal ganglia. However, this identification overlooks one of the most important features of the basal ganglia—the existence of a direct and an indirect pathway that compete against each other. This characteristic has important consequences in decision-making tasks, which are brought to light by Parkinson's disease (...) as well as genetic differences in dopamine receptors. This paper shows that a standard model of action selection in a cognitive architecture cannot replicate any of these findings, details an alternative solution that reconciles action selection in the architecture with the physiology of the basal ganglia, and extends the domain of application of cognitive architectures. The implication of this solution for other architectures and existing models are discussed. (shrink)

Synthetic biology presents a challenge to traditional accounts of biology: Whereas traditional biology emphasizes the evolvability, variability, and heterogeneity of living organisms, synthetic biology envisions a future of homogeneous, humanly engineered biological systems that may be combined in modular fashion. The present paper approaches this challenge from the perspective of the epistemology of technoscience. In particular, it is argued that synthetic-biological artifacts lend themselves to an analysis in terms of what has been called ‘thing knowledge’. As such, they (...) should neither be regarded as the simple outcome of applying theoretical knowledge and engineering principles to specific technological problems, nor should they be treated as mere sources of new evidence in the general pursuit of scientific understanding. Instead, synthetic-biological artifacts should be viewed as partly autonomous research objects which, qua their material-biological constitution, embody knowledge about the natural world—knowledge that, in turn, can be accessed via continuous experimental interrogation. (shrink)

Though only established as a discipline since the 1970s, philosophy of biology has already triggered investigations about its own history The Oxford handbook of philosophy of biology, Oxford University Press, New York, pp 11–33, 2008). When it comes to assessing the road since travelled—the research questions that have been pursued—manuals and ontologies also offer specific viewpoints, highlighting dedicated domains of inquiry and select work. In this article, we propose to approach the history of the philosophy of biology with a complementary (...) data-driven perspective that makes use of statistical algorithms applied to the complete full-text corpus of one major journal of the field—Biology and Philosophy—from its launch in 1986 up until 2017. By running text-mining and topic-modeling algorithms, we identified 67 key research topics that span across these 32 years. We also investigated the evolution of these topics over time and their fluctuating significance in the journal articles. Our results concur with known episodes or traits of the discipline—for instance, the significance of evolution-related topics or the decrease of articles with a marked historical dimension—but also highlight a diversity of topics that is much richer than what is usually acknowledged. (shrink)

Biological diversity would apparently seem the most intuitive and easily studied of all the ecological concepts. However, in practice biodiversity has suffered from great number of definitions that vary with the specific needs of the different researchers, thus making it extremely confusing as an ecological concept. In this paper, I shortly review the concept of biodiversity showing that there exists a substantial ambiguity among ecologists as far as biodiversity conceptualization and evaluation is concerned. I conclude that, due to this (...) major disagreement on its very nature, biodiversity may be defined simply as a set of multivariate summary statistics for quantifying different characteristics of community structure. (shrink)

The concepts of hierarchical organization, genetic determinism and biological specificity have played a crucial role in biology as a modern experimental science since its beginnings in the nineteenth century. The idea of genetic information and genetic determination was at the basis of molecular biology that developed in the 1940s with macromolecules, viruses and prokaryotes as major objects of research often labelled “reductionist”. However, the concepts have been marginalized or rejected in some of the research that in the late (...) 1960s began to focus additionally on the molecularization of complex biological structures and functions using systems approaches. This paper challenges the view that ‘molecular reductionism’ has been successfully replaced by holism and a focus on the collective behaviour of cellular entities. It argues instead that there are more fertile replacements for molecular ‘reductionism’, in which genomics, embryology, biochemistry, and computer science intertwine and result in research that is as exact and causally predictive as earlier molecular biology. (shrink)

Synthetic biology is an emerging technology that aims to design and engineer DNA and molecular structures of single cell organisms. Existing organisms can be altered, novel organisms can be created. In doing so, synthetic biology makes use of specific technoscientific understandings of living beings. This volume sets out to explore and assess synthetic biology and its notions of life from philosophical, ethical, social, and legal perspectives. Contents Concepts, Metaphors, Worldviews.- Public Good and Private Ownership.Social and Legal Ramifications.- Opportunities, Risks, Governance. (...) Target Groups Scholars of sociology, philosophy, theory of science, history of science, biology, engineering Politicians and policymakers The Editor Dr. Joachim Boldt is Deputy Director at the Institut für Ethik und Geschichte der Medizin in Freiburg, Germany. (shrink)

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

In this paper, I propose that time representation should be classified as agent dependent motor-intentional, agent dependent conceptual and agent independent conceptual. I employ this classification to explain certain features of psychological and cultural time and discuss how biological time constrains such features. The paper argues that motor-intentional time is a crucial psychophysical link that bridges the gap between purely biochemical cycles and conceptual-intentional representations of time, and proposes that the best way to understand the transitions from biological (...) to psychological time is to characterize them as phase transitions that emerge on the global properties of a system regardless of specific aspects of the underlying processing units. With respect to hierarchical models of time, the paper claims that although the hierarchical organization of constraints limits the number of possible instantiations of temporal information, informational phases have principles of organization of their own. Based on these proposals, I conclude that since information assembles itself into the temporal behavior of an agent, it is more accurate to call the principles governing such a behavioral unity a phase, rather than a hierarchy. To support these theses, the paper draws upon research in biology, neuroscience, philosophy and psychology. (shrink)

The process of condensation of an amorphous solid into a rigid matrix can often trap molecules in reversible binding sites. Exchange of the same molecular species with such sites is known to be sensitive to small chemical differences and to distinguish between enantiomers. In addition to their usefulness in chromatographic processes, such materials can separate, by solid phase extraction, specific compounds from complex mixtures. Furthermore, the trapped molecules can have their reactions guided and catalytically changed. The combination of this spontaneously (...) formed system of templates and catalytic sites may support a type of replication cycle, and suggests some pathways from simple chemistry toward the complexities of biology. © 2005 Wiley Periodicals, Inc. Complexity 11: 30–35, 2005 -/- . (shrink)

Biology, established around 1800 as the “science of life,” has developed as not only a specific scientific discipline but it has also continually served as a kind of social knowledge. Biological knowledge supported the modern order of the sexes and the two-sex model that it was structured along, as well as modern racism and multiple forms of social inequality articulated by dichotomizing the normal and abnormal. However, the fledgling discipline of biology alone was not capable of developing the epistemological (...) as well as political-ethical competence necessary for attaining this central status in the order of knowledge; it was possible only because philosophy and the emerging social sciences gave biology a specific status. The paper outlines the closely connected, but different attitudes of Kant and Schelling towards biological knowledge. While focusing on their different epistemic strategies towards the new form of nature knowledge, I also point to their different political-ethical articulations of biological knowledge. I conclude that a critical analysis of philosophies of nature around 1800 contributes not onlyto an understanding of the symbolic power of biology in the modern order of knowledge but also to rethinking philosophy’s relation to scientific knowledge today. (shrink)

Synthetic biology aims to synthesize novel biological systems or redesign existing ones. The field has raised numerous philosophical questions, but most especially what is novel to this field. In this article I argue for a novel take, since the dominant ways to understand synthetic biology’s specificity each face problems. Inspired by the examination of the work of a number of chemists, I argue that synthetic biology differentiates itself by a new regime of articulation, i.e. a new way of (...) articulating the questions and phenomena it wants to address. Instead of describing actual existing biological systems, the field aims to describe biological possibilities. In the second part I corroborate this hypothesis through a comparison between early research in the field of the origins of life and contemporary synthetic biologists, who are not so much interested in the historical origin of life on Earth, but rather in a universal biology of the possible origins of any life whatsoever. (shrink)

Invasion biology is a relatively young discipline which is important, interesting and currently in turmoil. Biological invaders can threaten native ecosystems and global biodiversity; they can incur massive economic costs and even introduce diseases. Invasion biologists generally agree that being able to predict when and where an invasion will occur is essential for progress in their field. However, successful predictions of this type remain elusive. This has caused a rift, as some researchers are pessimistic and believe that invasion biology (...) has no future, whereas others are more optimistic and believe that the key to successful prediction is the creation of a general, unified theoretical framework which encompasses all invasion events. Although I agree that there is a future for invasion biology, extensive synthesis is not the way to better predictions. I argue that the causes of invasion phenomena are exceedingly complex and heterogeneous, hence it is impossible to make generalizations over particular events without sacrificing causal detail. However, this causal detail is just what is needed for the specific predictions which the scientists wish to produce. Instead, I show that a limited type of synthesis is a more useful tool for generating successful predictions. An important implication of my view is that it points to a more pluralistic approach to invasion biology, where generalization and prediction are treated as important yet distinct research goals. (shrink)

This article explores how race, sexual attractiveness and ‘female nature’ are biologised in plastic surgery. I situate this analysis in relation to recent debates over the limits of social constructionism and calls for more engagement with biology in feminist theory and science studies. I analyse not only how the biological is represented by biomedicine, but also how it is experienced by patients and, most problematically, how it is entangled with social constructions of beauty, race and female reproduction. Drawing on (...) ethnographic fieldwork conducted in Brazil, I focus on plastic surgery, but also analyse how this specialty is linked to Ob-Gyn and endocrinology. I argue that medical procedures instantiate a biologised model of beauty I call ‘bare sex’ (Edmonds, 2010) that is defined in terms of racial traits, anatomy, reproductive processes, hormones and ‘secondary sexual traits’. While this is a historically specific model, it is also one that is inscribed on patients, altering anatomy and physiological processes. It thus has the potential to create a biological self-awareness that cannot fully be accounted for by a social constructionist analysis. (shrink)

ABSTRACT For Victoria Kahn, Hobbes' argument that fear of violent death is “the passion to be reckoned upon” in explaining what inclines men to peace must be interpreted as a mimetic argument. However, Kahn then notes a paradox that makes Hobbes' thinking problematic: whereas love and the desires are appetites that produce an imitative effect, fear is different. Though also a passion, fear lacks that capacity to produce a mimetic effect or, therefore, to generate a contract. My hypothesis is that (...) resolving the dilemma presented in Kahn's interpretation of Hobbes requires a shift in attention from mimesis to rhetoric and, more specifically, to biological rhetoric as defined by Nancy Struever. This approach to Hobbes makes it possible to understand the rhetorical role of fear in generating and maintaining the social contract, and how the problem that Kahn signals—the impotence of fear in relation to mimesis—can be resolved. (shrink)

We address the question of whether and to what extent explanatory and modelling strategies in systems biology are mechanistic. After showing how dynamic mathematical models are actually required for mechanistic explanations of complex systems, we caution readers against expecting all systems biology to be about mechanistic explanations. Instead, the aim may be to generate topological explanations that are not standardly mechanistic, or to arrive at design principles that explain system organization and behaviour in general, but not specific mechanisms. These abstraction (...) strategies serve various aims, including prediction and control, that are central to understanding the epistemic diversity of systems biology. (shrink)

The engineering-based approach of synthetic biology is characterized by an assumption that ‘engineering by design’ enables the construction of ‘living machines’. These ‘machines’, as biological machines, are expected to display certain properties of life, such as adapting to changing environments and acting in a situated way. This paper proposes that a tension exists between the expectations placed on biological artefacts and the notion of producing such systems by means of engineering; this tension makes it seem implausible that (...) class='Hi'>biological systems, especially those with properties characteristic of living beings, can in fact be produced using the specific methods of engineering. We do not claim that engineering techniques have nothing to contribute to the biotechnological construction of biological artefacts. However, drawing on Descartes’s and Kant’s thinking on the relationship between the organism and the machine, we show that it is considerably more plausible to assume that distinctively biological artefacts emerge within a paradigm different from the paradigm of the Cartesian machine that underlies the engineering approach. We close by calling for increased attention to be paid to approaches within molecular biology and chemistry that rest on conceptions different from those of synthetic biology’s engineering paradigm. (shrink)

Biological regulation is what allows an organism to handle the effects of a perturbation, modulating its own constitutive dynamics in response to particular changes in internal and external conditions. With the central focus of analysis on the case of minimal living systems, we argue that regulation consists in a specific form of second-order control, exerted over the core regime of production and maintenance of the components that actually put together the organism. The main argument is that regulation requires a (...) distinctive architecture of functional relationships, and specifically the action of a dedicated subsystem whose activity is dynamically decoupled from that of the constitutive regime. We distinguish between two major ways in which control mechanisms contribute to the maintenance of a biological organisation in response to internal and external perturbations: dynamic stability and regulation. Based on this distinction an explicit definition and a set of organisational requirements for regulation are provided, and thoroughly illustrated through the examples of bacterial chemotaxis and the lac-operon. The analysis enables us to mark out the differences between regulation and closely related concepts such as feedback, robustness and homeostasis. (shrink)

This essay explores the universal cognitive bases of biological taxonomy and taxonomic inference using cross-cultural experimental work with urbanized Americans and forest-dwelling Maya Indians. A universal, essentialist appreciation of generic species appears as the causal foundation for the taxonomic arrangement of biodiversity, and for inference about the distribution of causally-related properties that underlie biodiversity. Universal folkbiological taxonomy is domain-specific: its structure does not spontaneously or invariably arise in other cognitive domains, like substances, artifacts or persons. It is plausibly an (...) innately-determined evolutionary adaptation to relevant and recurrent aspects of ancestral hominid environments, such as the need to recognize, locate, react to, and profit from many ambient species. Folkbiological concepts are special players in cultural evolution, whose native stability attaches to more variable and difficult-to-learn representational forms, thus enhancing the latter's prospects for regularity and recurrence in transmission within and across cultures. This includes knowledge that cumulatively enriches (folk expertise), overrides (religious belief) or otherwise transcends (science) the commonsense ontology prescribed by folkbiology. Finally, the studies summarized here indicate that results gathered from “standard populations” in regard to biological categorization and reasoning more often than not fail to generalize in straightforward ways to humanity at large. This suggests the need for much more serious attention to cross-cultural research on basic cognitive processes. (shrink)

This essay in the "anthropology of science" is about how cognition constrains culture in producing science. The example is folk biology, whose cultural recurrence issues from the very same domain-specific cognitive universals that provide the historical backbone of systematic biology. Humans everywhere think about plants and animals in highly structured ways. People have similar folk-biological taxonomies composed of essence-based species-like groups and the ranking of species into lower- and higher-order groups. Such taxonomies are not as arbitrary in structure and (...) content, nor as variable across cultures, as the assembly of entities into cosmologies, materials or social groups. (shrink)

This article aims to make an analysis of the cultural and anthropological issues raised by synthetic biology. The novelty of the field makes it relatively difficult to compose a comprehensive analysis, even for philosophers with experience, but who are not familiar with the specifics of the field. The article will follow the synthesis of the models of ethical decision applicable in the field of ethical evaluation of technologies from a cultural and anthropological perspective, their critical analysis and will highlight the (...) limitations of each model, as well as a possible synthesis of a model of ethical evaluation of technologies. Afterwords, it can be decided whether a particular technology - such as those involved in synthetic biology - poses risks to the environment, to those involved in research, to future generations, to humanity as a whole or to present or future ecosystems. (shrink)