This paper argues that the biochemistry of memory consolidation provides valuable model systems for exploring the multiple realization of psychological states.

This paper investigates the interface between philosophy and biochemistry. While it is problematic to justify the application of a particular philosophical model to biochemistry, it seems to be even more difficult to develop a special “Philosophy for Biochemistry”. Alternatively, philosophy can be used in biochemistry based on an alternative approach that involves an interdependent iteration process at a philosophical and (bio)chemical level (“Exeter Method”). This useful iteration method supplements more abstract approaches at the (...) interface between philosophy and natural sciences, and serves the biochemical community to systematically locate logical inconsistencies that arise from more theoretical aspects of the scientific process. Initial cycles of this iteration process identify the in vitro–in vivo problem as a central epistemological difficulty in biochemical research. While previous attempts have generated ad hoc rules to mend the gap between chemistry, biochemistry and biology in order to justify in vitro experimentation, this paper concludes that in vitro experimentation is heavily based on chemistry and cannot derive definite statements about biological processes. It can, however, generate results that will influence the direction of future biological research. The consequence is that the relationship between in vitro and in vivo experimentation is more of a psychological or social one than of a logical nature. Apart from highlighting these inconsistencies in biochemical thinking (“problem awareness”), the Exeter Method demands an improvement of biochemical terminology that contains separate and unequivocally defined terms for in vitro and in vivo systems. (shrink)

Scientific development influences philosophical thought, and vice versa. If philosophy is to be of any use to the production, evaluation or application of biochemical knowledge, biochemistry will have to explicate its needs. This paper concentrates on the need for a philosophical analysis of methodological challenges in biochemistry, above all the problematic relation between in vitro experiments and the desire for in vivo knowledge. This problem receives much attention within biochemistry, but the focus is on practical detail. (...) It is discussed how a theoretical analysis can go beyond a naïve understanding of scientific success and failure in such cases. Several examples are presented to elucidate this issue, including the methodological implications of the precautionary principle, the possible interplay between theoretical methodology of biochemistry and the science studies, and the methodological complexities related to experimental protocol standardisation and use of instruments and kits. (shrink)

The history of biochemistry and molecular biology is replete with examples of erroneous theories that persisted for considerable lengths of time before they were rejected. This paper examines patterns of dissolution of three such erroneous hypotheses: The idea that nucleic acids are tetrads of the four nucleobases (‘the tetranucleotide hypothesis’); the notion that proteins are collinear with their encoding genes in all branches of life; and the hypothesis that proteins are synthesized by reverse action of proteolytic enzymes. Analysis of (...) these cases indicates that amassed contradictory empirical findings did not prompt critical experimental testing of the prevailing theories nor did they elicit alternative hypotheses. Rather, the incorrect models collapsed when experiments that were not purposely designed to test their validity exposed new facts. (shrink)

In this essay we take creationist biochemist Michael Behe to task for failing to make an evidentially grounded case for the supernatural intelligent design of biochemical systems. In our earlier work on Behe we showed that there were dimensions to biochemical complexity---redundant complexity---that he appeared to have ignored. Behe has recently replied to that work. We show here that his latest arguments contain fundamental flaws.

Scientists and historians have often presumed that the divide between biochemistry and molecular biology is fundamentally epistemological.100 The historiography of molecular biology as promulgated by Max Delbrück's phage disciples similarly emphasizes inherent differences between the archaic tradition of biochemistry and the approach of phage geneticists, the ur molecular biologists. A historical analysis of the development of both disciplines at Berkeley mitigates against accepting predestined differences, and underscores the similarities between the postwar development of biochemistry and the emergence (...) of molecular biology as a university discipline. Stanley's image of postwar biochemistry, with its focus on viruses as key experimental systems, and its preference for following macromolecular structure over metabolism pathways, traced the outline of molecular biology in 1950.Changes in the postwar political economy of research universities enabled the proliferation of disciplines such as microbiology, biochemistry, biophysics, immunology, and molecular biology in universities rather than in medical schools and agricultural colleges. These disciplines were predominantly concerned with investigating life at the subcellular level-research that during the 1930s had often entailed collaboration with physicists and chemists. The interdisciplinary efforts of the 1930s (many fostered by the Rockefeller Foundation) yielded a host of new tools and reagents that were standardized and mass-produced for laboratories after World War II. This commercial infrastructure enabled “basic” researchers in biochemistry and molecular biology in the 1950s and 1960s to become more independent from physics and chemistry (although they were practicing a physicochemical biology), as well as from the agricultural and medical schools that had previously housed or sponsored such research. In turn, the disciplines increasingly required their practitioners to have specialized graduate training, rather than admitting interlopers from the physical sciences.These general transitions toward greater autonomy for biochemistry and allied disciplines should not mask the important particularities of these developments on each campus. At the University of Caliornia at Berkeley, agriculture had provided, with medicine, significant sponsorship for biochemistry. The proximity of Lawrence and his cyclotrons supported the early development of Berkeley as a center for the biological uses of radioisotopes, particularly in studies of metabolism and photosynthesis. Stanley arrived to establish his department and virus institute before large-scale federal funding of biomedical research was in place, and he courted the state of California for substantial backing by promising both national prominence in the life sciences and virus research pertinent to agriculture and public health. Stanley's venture benefited significantly from the expansion of California's economy after World War II, and his mobilization against viral diseases resonated with the concerns of the Cold War, which fueled the state's rapid growth. The scientific prominence of contemporary developments at Caltech and Stanford invites the historical examination of the significance of postwar biochemistry and molecular biology within the political and cultural economy of the Golden State.In 1950, Stanley presented a persuasive picture of the power of biochemistry to refurbish life science at Berkeley while answering fundamental questions about life and infection. In the words of one Rockefeller Foundation officer,There seems little doubt in [my] mind that as a personality Stanley will be well able to dominate the other personalities on the Berkeley campus and will be able to drive his dream through to completion, which, incidentally, leaves Dr. Hubert [sic] Evans and the whole ineffective Life Sciences building in the somewhat peculiar position of being by-passed by much of the truly modern biochemistry and biophysics research that will be carried out at Berkeley. Furthermore, it seems likely that Dr. S's show will throw Dr. John Lawrence's Biophysics Department strongly in the shade both figuratively and literally, but should make the University of California pre-eminent not only in physics but in biochemistry as well.101Stanley, Sproul, Weaver, and this officer (William Loomis) all testified to a perceptible postwar opportunity to capitalize on public support for biological research that relied on the technologies from physics and chemistry without being captive to them, and that addressed issues of medicine and agriculture without being institutionally subservient. What is striking, given the expectation by many that Stanley would ‘be able to drive his dream through to completion,” was that in fact he did not. Biochemists who had succeeded in making their expertise valued in specialized niches were resistant to giving up their affiliations to joint Stanley's “liberated” organization. Stanley's failure was not simply due to institutional factors: researchers as well as Rockefeller Foundation officers faulted him for his lack of scientific imagination, which made it difficult for him to gain credibility in leading the field. Moreover, many biochemists did not share Stanley's commitment to viruses as the key material for the “new biochemistry.”In the end, Stanley's free-standing department did become a first-rate department of biochemistry, but only after freeing itself from Stanley's leadership and his single-minded devotion to viruses. Nonetheless, the falling-out with the Berkeley biochemists was rapidly followed by the establishment of a Department of Molecular Biology, attesting to the unabating economic and institutional possibilities for an authoritative “general biology” (or two, for that matter) to take hold. In each case, following Stanley's dream sheds light on how the possible and the real shaped the (re)formation of biochemistry and molecular biology as postwar life sciences. (shrink)

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

According to process ontology in the philosophy of biology, the living world is better understood as processes rather than as substantial individuals. Within this perspective, an organism does not consist of a hierarchy of structures like a machine, but rather a dynamic hierarchy of processes, dynamically maintained and stabilized at different time scales. With this respect, two processual approaches on enzymes by Stein (Hyle Int J Philos Chem 10(4):5–22, 2004, Process Stud 34:62–80, 2005, Found Chem 8:3–29, 2006) and by (...) Guttinger (Everything Flows: Towards a Processual Philosophy of Biology, Oxford University Press, Oxford, 2018) allows to think of macromolecules as relational and processual entities. In this work, I propose to extend their arguments to another case study within the biochemical domain, which is the case of ligand receptors and receptor-mediated biosignaling. The aim of this work is to analyze the case of G Protein-Coupled Receptors and biosignaling under the consideration of a processual ontology. I will defend that the processual ontology framework is adequate for the biochemical domain and that it allows accounting for the current biochemical knowledge related to the case study. (shrink)

Popper's critical rationalism is widely accepted under scientists and philosophers of science as a proper method for the reconstruction of scientific theories. On occasion of the application of the Popperian ideas for the reconstruction of chemistry by Akeroyd the flaws of the critical rationalist approach are criticised and a methodical alternative is proposed, involving the operational definition of scientific terms.

Philosophers of science diverge on the question what drives the growth of scientific knowledge. Most of the twentieth century was dominated by the notion that theories propel that growth whereas experiments play secondary roles of operating within the theoretical framework or testing theoretical predictions. New experimentalism, a school of thought pioneered by Ian Hacking in the early 1980s, challenged this view by arguing that theory-free exploratory experimentation may in many cases effectively probe nature and potentially spawn higher evidence-based theories. Because (...) theories are often powerless to envisage workings of complex biological systems, theory-independent experimentation is common in the life sciences. Some such experiments are triggered by compelling observation, others are prompted by innovative techniques or instruments, whereas different investigations query big data to identify regularities and underlying organizing principles. A distinct fourth type of experiments is motivated by a major question. Here I describe two question-guided experimental discoveries in biochemistry: the cyclic adenosine monophosphate mediator of hormone action and the ubiquitin-mediated system of protein degradation. Lacking underlying theories, antecedent data bases, or new techniques, the sole guides of the two discoveries were respective substantial questions. Both research projects were similarly instigated by theory-free exploratory experimentation and continued in alternating phases of results-based interim working hypotheses, their examination by experiment, provisional hypotheses again, and so on. These two cases designate theory-free, question-guided, stepwise biochemical investigations as a distinct subtype of the new experimentalism mode of scientific enquiry. (shrink)

The discovery of RNA interference in 1998 has made a lasting impact on biological research. Identifying the regulatory role of small RNAs changed the modes of molecular biological inquiry as well as biologists' understanding of genetic regulation. This article examines the early years of small RNA biology's success story. I query which factors had to come together so that small RNA research came into life in the blink of an eye. I primarily look at scientific repertoires as facilitators of rapid (...) scientific change. I show that for a short period of time, between the years 1998 and 2002, different model organism communities, investigative strategies, technological innovations, and research interests could be successfully aligned to take small RNA research off the ground. I discuss how the keystone discoveries were situated in specific experimental traditions and what strategies were employed to establish these discoveries as more general phenomena. Providing thus a practice-based approach of rapid scientific change, I ask how to relate the change in propositional bits of scientific knowledge with changes in scientific practice. (shrink)

Kincaid argues that molecular biology provides little support for the reductionist program, that biochemistry does not reveal common mechanisms, indeed that biochemical theory obstructs discovery. These assertions clash with biologists' stated advocacy of reductionist programs and their claims about the consequent unity of experimental biology. This striking disagreement goes beyond differences in meaning granted to the terms. More significant is Kincaid's misunderstanding of what biochemists do, for a closer look at scientific practice-- and one of Kincaid's examples--reveals substantial progress (...) toward explaining biological function with biochemical models. With the molecular detail emerge unifying generalizations as well as further aspects of the functional processes. (shrink)

According to process ontology in the philosophy of biology, the living world is better understood as processes rather than as substantial individuals. Within this perspective, an organism does not consist of a hierarchy of structures like a machine, but rather a dynamic hierarchy of processes, dynamically maintained and stabilized at different time scales. With this respect, two processual approaches on enzymes by Stein (Hyle Int J Philos Chem 10(4):5–22, 2004, Process Stud 34:62–80, 2005, Found Chem 8:3–29, 2006) and by (...) Guttinger (Everything Flows: Towards a Processual Philosophy of Biology, Oxford University Press, Oxford, 2018) allows to think of macromolecules as relational and processual entities. In this work, I propose to extend their arguments to another case study within the biochemical domain, which is the case of ligand receptors and receptor-mediated biosignaling. The aim of this work is to analyze the case of G Protein-Coupled Receptors and biosignaling under the consideration of a processual ontology. I will defend that the processual ontology framework is adequate for the biochemical domain and that it allows accounting for the current biochemical knowledge related to the case study. (shrink)

Biological systems exhibit complexity at all levels of organization. It has recently been argued by Michael Behe that at the biochemical level a type of complexity exists--irreducible complexity--that cannot possibly have arisen as the result of natural, evolutionary processes and must instead be the product of (supernatural) intelligent design. Recent work on self-organizing chemical reactions calls into question Behe's analysis of the origins of biochemical complexity. His central interpretative metaphor for biochemical complexity, that of the well-designed mousetrap that ceases to (...) function if critical parts are absent, is undermined by the observation that typical biochemical systems exhibit considerable redundancy and overlap of function. Real biochemical systems, we argue, manifest redundant complexity--a characteristic result of evolutionary processes. (shrink)

This volume connects chemistry and philosophy in order to face questions raised by chemistry in our present world. The idea is first to develop a kind of philosophy of chemistry which is deeply rooted in the exploration of chemical activities. We thus work in close contact with chemists. Following this line of reasoning, the first part of the book encourages current chemists to describe their workaday practices while insisting on the importance of attending to methodological, metrological, philosophical, and (...) epistemological questions related to their activities. It deals with sustainable chemistry, chemical metrology, nanochemistry, and biochemistry, among other crucial topics. In doing so, those chemists invite historians and philosophers to provide ideas for future developments. In a nutshell, this part is a call for forthcoming collaborations focused on instruments and methods, that is on ways of doing chemistry. The second part of the book illustrates the multifarious ways to study chemistry and even proposes new approaches to doing so. Each approach is interesting and incomplete but the emergent whole is richer than any of its components. Analytical work needs socio-historical expertise as well as many other approaches in order to keep on investigating chemistry to greater and greater depth. This heterogeneity provides a wide set of methodological perspectives not only about current chemical practices but also about the ways to explore them philosophically. Each approach is a resource to study chemistry and to reflect upon what doing philosophy of science can mean. In the last part of the volume, philosophers and chemists propose new concepts or reshape older ones in order to think about chemistry. The act of conceptualization itself is queried as well as the relationships between concepts and chemical activities. Prefaced by Nobel Laureate in Chemistry, Roald Hoffmann, and by the President of the International Society for the Philosophy of Chemistry, Rom Harrè, this volume is a plea for the emergence of a collective cleverness and aims to foster inventiveness. (shrink)

This book is a collection of papers which reflect the recent trends in the philosophy and history of molecular biology. It brings together historians, philosophers, and molecular biologists who reflect on the discipline's emergence in the 1950's, its explosive growth, and the directions in which it is going. Questions addressed include: (i) what are the limits of molecular biology? (ii) What is the relation of molecular biology to older subdisciplines of biology, especially biochemistry? (iii) Are there theories in (...) molecular biology? (iv) If so, how are these theories structured? (v) What role did information theory play in the rise of molecular biology? The book will open the way for many future researchers. (shrink)

This paper analyzes the interaction between science, philosophy and politics (including ideology) in the early work of J. B. S. Haldane (from 1922 to 1937). This period is particularly important, not only because it is the period of Haldane's most significant biological work (both in biochemistry and genetics), but also because it is during this period that his philosophical and political views underwent their most significant transformation. His philosophical stance first changed from a radical organicism to a position (...) far more compatible with mechanical materialism. The primary intellectual influence that was responsible for this shift was that of F. G. Hopkins. Later, Haldane came to accept Marxism and its official metaphysics, dialectical materialism, a move that let him accept the materialist conception of the world while still maintaining a resolute distance from mechanism. Throughout all these changes, what is most obvious is the influence of science on Haldane's philosophical views. An influence in the opposite direction is far less apparent. (shrink)

In lieu of an abstract, here is a brief excerpt of the content:The Philosophy of George Engel and the Philosophy of MedicineJeffrey P. Spike (bio)KeywordsGeorge Engel, psychosocial medicine, medical education, medical humanities, interviewing skills, philosophy of medicine, scientific methodDoctor Brad Lewis has encouraged us to consider George Engel’s philosophy with his excellent essay on Engel and Pragmatism. As a philosopher teaching full time in a medical school, it is refreshing to have an opportunity to analyze the (...) work of two physicians at this level of reflection and abstraction. It is even more of a pleasure because I knew Dr. Engel personally while I was teaching at the University of Rochester School of Medicine. I will make some observations of the philosophy behind Dr. Engel’s work, both published and practical, that is, as reflected in his writing but also in his influence in the medical curriculum at the institution that he called home for some thirty years (as seems appropriate when considering someone’s bona fides as a pragmatist).Engel’s Philosophy and Medicine’s PhilosophyGeorge Engel’s primary philosophical concern was to fight the powerful belief (or perhaps delusion) that medicine was evolving into a pure physical science, an extension of biochemistry and cell biology, or as we would now call them, proteomics and genomics. There is little evidence that he espoused any one methodology for basic science, so much as he opposed any one methodology for medicine. So to say he was a pragmatist seems underdetermined by his words, if that is taken to mean he advocated for changing the methodological model for scientific research. Rather the question is whether his preferred medical methodology is best characterized as pragmatic, or by some other description. On that score I agree with Lewis wholeheartedly.Of course, it might be that the claim of pragmatism is not meant to suggest a change in method for basic science, but to advocate for retaining an appreciation for the whole range of approaches to knowledge, from experimental science to epidemiology, and from epidemiology to acculturation. By that definition of pragmatism, Engel was indeed a pragmatist. Interpreted this way, he wanted medicine to stop worshipping the scientific method and appreciate that there are many paths to knowledge besides through the wet lab.It might be said that there are different scientific methods for different sciences, and Engel wanted us to appreciate that the reductionist methods [End Page 315] appropriate to the sciences of the small are not necessarily methods that can be applied to all sizes of objects we study, or all levels of reality (like the psychological and social). This is the truth about the world, although I am not sure that this is what Engel meant. As Lewis notes, Engel’s writing does sometimes sound as if he worshipped at the alter of science, as if all subjects of importance can be studied scientifically. But if he believed that, he was not correct. It might be, if all the subjects of the university that Lewis mentions are important, that some will turn out to be able to be studied in academically rigorous methods that are not scientific in any of the usual meanings of the word. Consider philosophy itself, for example.To the degree that it may stretch the evidence to say that Engel would have advocated for a pragmatic scientific method, it is still the case that pragmatism as outlined by Lewis and Engel’s biopsychosocial model can both be used to help medicine understand itself and overcome the temptation to idolize science. Medicine is not a science, or at least it is not just a science; in fact, I would suggest that it never was a science, and it will never be a science. Medicine is about health and illness, and uses whatever science it can to promote health and to treat (ameliorate or cure) illness.None of this should necessarily lead us to idolize pragmatism either. If each subject has its own ideal methodology for study, then it may be that pragmatism is the preferred method for, say, clinical judgment, whereas the scientific method is the best for the ‘hard’ sciences, and logic for philosophy. Or perhaps pragmatism and inductive logic are competing models for clinical... (shrink)

This volume follows the successful book, which has helped to introduce and spread the Philosophy of Chemistry to a wider audience of philosophers, historians, science educators as well as chemists, physicists and biologists. The introduction summarizes the way in which the field has developed in the ten years since the previous volume was conceived and introduces several new authors who did not contribute to the first edition. The editors are well placed to assemble this book, as they are the (...) editor in chief and deputy editors of the leading academic journal in the field, Foundations of Chemistry. The philosophy of chemistry remains a somewhat neglected field, unlike the philosophy of physics and the philosophy of biology. Why there has been little philosophical attention to the central discipline of chemistry among the three natural sciences is a theme that is explored by several of the contributors. This volume will do a great deal to redress this imbalance. Among the themes covered is the question of reduction of chemistry to physics, the reduction of biology to chemistry, whether true chemical laws exist and causality in chemistry. In addition more general questions of the nature of organic chemistry, biochemistry and chemical synthesis are examined by specialist in these areas. (shrink)

Talk of mechanisms is ubiquitous in the natural sciences. Interdisciplinary fields such as biochemistry and pharmacy frequently discuss mechanisms with the assistance of diagrams. Such diagrams usually depict entities as structures or boxes and activities or interactions as arrows. While some of these arrows may indicate causal or componential relations, others may represent temporal or operational orders. Importantly, what kind of relation an arrow represents may not only vary with context but also be underdetermined by empirical data. In this (...) manuscript, we investigate how an analysis of pharmacological mechanisms in terms of producing and underlying mechanisms—as discussed in the contemporary philosophy of science—may shed light on these issues. Specifically, we shall argue that while pharmacokinetic mechanisms usually describe causal chains of production, pharmacodynamics tends to focus on mechanisms of action underlying the in vivo effects of a drug. Considering the action of thyroid gland hormones in the human body as a case study, we further demonstrate that pharmacodynamic schemes tend to incorporate entities and interactions on multiple levels. Yet, traditional pharmacodynamic schemes are sketched “flat”, i.e., non-hierarchically. We suggest that transforming flat pharmacodynamic schemes into mechanistic multi-level representations may assist in disentangling the different kinds of mechanisms and relations depicted by arrows in flat schemes. The resulting Baumkuchen model provides a powerful and practical alternative to traditional flat schemes, as it explicates the relevant mechanisms and relations more clearly. On a more general note, our discussion demonstrates how pharmacology and related disciplines may benefit from applying concepts from the new mechanist philosophy to guide the interpretation of scientific diagrams. (shrink)

The Other Perennial Philosophy: A Metaphysical Dialectic seeks to synthesize the many fields within science, philosophy, and religion to achieve the most comprehensive picture ever constructed to incorporate universally held beliefs about God, man, and the universe. This book attempts to accomplish several interrelated purposes: to describe the Perennial Philosophy in its depth; to analyze the critical elements contained within such a body of thought; to bring to light the vast literature of views which are oppositional, at (...) least on some level, to those contained in the Perennial Philosophy; to synthesize these seemingly discordant thoughts into a new vision of the nature of reality; to dissect the implications of this new model; and lastly and perhaps most importantly, to demonstrate that intellect has no innate constraints. This book rigorously explores the connections to be made by weaving together the threads of philosophy, religious theology, mysticism, mythology, mathematics, physics, and biochemistry. In this study is both a critique and an homage to Perennial Philosophy. In evoking a new vision of reality, which is at the same time a modernized version of an old image, The Other Perennial Philosophy: A Metaphysical Dialectic seeks to entice readers to rethink their own views on a subject of crucial importance to all. This book will appeal to anyone interested in philosophy and religion. (shrink)

Discovery proceeds in stages of construction, evaluation, and revision. Each of these stages is constrained by what is known or conjectured about what is being discovered. A new characterization of mechanism aids in specifying what is to be discovered when a mechanism is sought. Guidance in discovering mechanisms may be provided by the reasoning strategies of schema instantiation, modular subassembly, and forward/backward chaining. Examples are found in mechanisms in molecular biology, biochemistry, immunology, and evolutionary biology.

Bernard Lonergan identified the need and possibility of what he called "generalized empirical method" in science and philosophy. Implementation will be a future community achievement. The book enters into details of a selection of examples in the sciences and philosophy of science. These are provided not to engage in, or blend the present aim with traditional philosophical debate, but as points of entry to help reveal the possibility and need of balanced empirical method. Taking words of Lonergan: "(Q)uestions (...) of method are practical. So my purpose in these (chapters) is not to demonstrate what is necessary. It is not to forecast what is probable. It is... to invite you to share in the exploration of a proposal" (Bernard Lonergan, A Third Collection (1985), 114). The main examples are drawn from biochemistry and biology, although heuristics envisioned will include all sciences. (shrink)

On the whole our study has made a plea for the combined research into the history, methodology and philosophy of science. There is an intricate communication between these aspects of science, philosophy being both a fruit of scientific developments and a higher-level frame of reference for discussion on the inevicable metaphysical issues in science.As such philosophy can be very useful to science, but should never impose its ideas on the conduct of scientists . ... Zie: Summary.

Scientific models share one central characteristic with fiction: their relation to the physical world is ambiguous. It is often unclear whether an element in a model represents something in the world or presents an artifact of model building. Fiction, too, can resemble our world to varying degrees. However, we assign a different epistemic function to scientific representations. As artifacts of human activity, how are scientific representations allowing us to make inferences about real phenomena? In reply to this concern, philosophers of (...) science have started analyzing scientific representations in terms of fictionalization strategies. Many arguments center on a dyadic relation between the model and its target system, focusing on structural resemblances and “as if” scenarios. This chapter provides a different approach. It looks more closely at model building to analyze the interpretative strategies dealing with the representational limits of models. How do we interpret ambiguous elements in models? Moreover, how do we determine the validity of model-based inferences to information that is not an explicit part of a representational structure? I argue that the problem of ambiguous inference emerges from two features of representations, namely their hybridity and incompleteness. To distinguish between fictional and non-fictional elements in scientific models my suggestion is to look at the integrative strategies that link a particular model to other methods in an ongoing research context. To exemplify this idea, I examine protein modeling through X-ray crystallography as a pivotal method in biochemistry. (shrink)

Reasoning in Biological Discoveries brings together a series of essays, which focus on one of the most heavily debated topics of scientific discovery. Collected together and richly illustrated, Darden's essays represent a groundbreaking foray into one of the major problems facing scientists and philosophers of science. Divided into three sections, the essays focus on broad themes, notably historical and philosophical issues at play in discussions of biological mechanism; and the problem of developing and refining reasoning strategies, including interfield relations and (...) anomaly resolution. Darden summarizes the philosophy of discovery and elaborates on the role that mechanisms play in biological discovery. Throughout the book, she uses historical case studies to extract advisory reasoning strategies for discovery. Examples in genetics, molecular biology, biochemistry, immunology, neuroscience and evolutionary biology reveal the process of discovery in action. (shrink)

Scientific progress is one of the most popular topics in philosophy of science. Currently, the area offers a range of models to choose scientific progress, when addressing the specific processes that occurred in a particular discipline of science. In this article we analyze the notion of theoretical change in biochemistry, but translatable to biology and biomedical sciences by making use of the pull of theories, under one of the prospects of scientific progress, P. Kitcher, which we believe is (...) one of the best to shed clarity to the discussion of the case. (shrink)

From the school yard to the workplace, there’s no charge more damning than “you’re being unfair!” Born out of democracy and raised in open markets, fairness has become our de facto modern creed. The very symbol of American ethics—Lady Justice—wears a blindfold as she weighs the law on her impartial scale. In our zealous pursuit of fairness, we have banished our urges to like one person more than another, one thing over another, hiding them away as dirty secrets of our (...) humanity. In Against Fairness, polymath philosopher Stephen T. Asma drags them triumphantly back into the light. Through playful, witty, but always serious arguments and examples, he vindicates our unspoken and undeniable instinct to favor, making the case that we would all be better off if we showed our unfair tendencies a little more kindness—indeed, if we favored favoritism. Conscious of the egalitarian feathers his argument is sure to ruffle, Asma makes his point by synthesizing a startling array of scientific findings, historical philosophies, cultural practices, analytic arguments, and a variety of personal and literary narratives to give a remarkably nuanced and thorough understanding of how fairness and favoritism fit within our moral architecture. Examining everything from the survival-enhancing biochemistry that makes our mothers love us to the motivating properties of our “affective community,” he not only shows how we favor but the reasons we should. Drawing on thinkers from Confucius to Tocqueville to Nietzsche, he reveals how we have confused fairness with more noble traits, like compassion and open-mindedness. He dismantles a number of seemingly egalitarian pursuits, from classwide Valentine’s Day cards to civil rights, to reveal the envy that lies at their hearts, going on to prove that we can still be kind to strangers, have no prejudice, and fight for equal opportunity at the same time we reserve the best of what we can offer for those dearest to us. Fed up with the blue-ribbons-for-all absurdity of "fairness" today, and wary of the psychological paralysis it creates, Asma resets our moral compass with favoritism as its lodestar, providing a strikingly new and remarkably positive way to think through all our actions, big and small. (shrink)

As a scientist, philosopher and scholar in Jewish thought, Yeshayahu Leibowitz was one of the most noteworthy Jewish thinkers in the twentieth century. He was endowed with an remarkable intellect and was knowledgeable across a variety of fields. Born in Riga (Latvia) in 1903 he later immigrated to Israel, where he taught Organic chemistry, biochemistry, neurology, biology, neurophysiology, philosophy and Jewish thought at Haifa and Jerusalem University. He was chief editor of the Hebrew encyclopedia, where he wrote about (...) scientific, philosophical, historical and religious topics. Leibowitz was an orthodox Jew but rejected the notion of divine intervention in nature or history. So what was actually Leibowitz' belief? This is what this book is about. (shrink)

While the phrase "metaphysics of science" has been used from time to time, it has only recently begun to denote a specific research area where metaphysics meets philosophy of science—and the sciences themselves. The essays in this volume demonstrate that metaphysics of science is an innovative field of research in its own right. The principle areas covered are: The modal metaphysics of properties: What is the essential nature of natural properties? Are all properties essentially categorical? Are they all essentially (...) dispositions, or are some categorical and others dispositional? Realism in mathematics and its relation to science: What does a naturalistic commitment of scientific realism tell us about our commitments to mathematical entities? Can this question be framed in something other than a Quinean philosophy? Dispositions and their relation to causation: Can we generate an account of causation that takes dispositionality as fundamental? And if we take dispositions as fundamental, what is the ontological ground of dispositions? Pandispositionalism: Could all properties be dispositional in nature? Natural kinds: Are there natural kinds, and if so what account of their nature should we give? For example, do they have essences? Here we consider how these issues may be illuminated by considering examples from reals science, in particular biochemistry and neurobiology. (shrink)

This volume gathers scholars from ecology, biochemistry, evolutionary biology, cognitive science, anthropology and philosophy to discuss how Gregory Bateson's thinking might lead to a reframing of central problems in modern science.

The objective of the new series, "Molecular Biology, Biochemistry and Biophysics", of which this brochure forms the first volume, is to produce more than another compilation of data. It is hoped that the new series will help the individual "specialist" keep abreast of important developments in the natural sciences at the molecular and subcellular level in fields complementary to his own. The predominant aim is not so much to increase the ever-growing body of information in an encyclopedic fashion but (...) rather to give, in addition to a well rounded factual presentation of subjects which have reached a degree of maturation, a leitmotiv developed by the individual authors from a more personal point of view. The reader should thus be able to use these mono graphs not only for acquisition of knowledge but as a source of further motiva tion in his own work. This latter and more consequential aim of the monograph series is one of the reasons for presenting here a most unusual talk which should enable the reader to sit back and view his own efforts in the context of science and creative attempts as a whole. The lecture is the virtually unknown inaugural address of the Dutch physical chemist JACOBUS HENRICUS VAN'T HOFF. As is shown in his short biography presented on pages 3 and 4 the principal thoughts of the molecular biologist of today are akin to his own and he clearly recognized the universality of molecular life processes. (shrink)

This volume reviews examples and notions of robustness at several levels of biological organization. It tackles many philosophical and conceptual issues and casts an outlook on the future challenges of robustness studies in the context of a practice-oriented philosophy of science. The focus of discussion is on concrete case studies. These highlight the necessity of a level-dependent description of robust biological behaviors.Experts from the neurosciences, biochemistry, ecology, biology, and the history and the philosophy of life sciences provide (...) a multiplex perspective on the topic. Contributions span from protein folding, to cell-level robustness, to organismal and developmental robustness, to sensorimotor systems, up to the robustness of ecological systems.Several chapters detail neurobiological case-studies. The brain, the poster child of plasticity in biology, offers multiple examples of robustness. Neurobiology explores the importance of temporal organization and multiscalarity in making this robustness-with-plasticity possible. The discussion also includes structures well beyond the brain, such as muscles and the complex feedback loops involved in the peculiar robustness of music perception. Overall, the volume grounds general reflections upon concrete case studies, opening to all the life sciences but also to non-biological and bio-inspired fields such as post-modern engineering. It will appeal to researchers, students, as well as non-expert readers. (shrink)

Empirical success is a central criterion for scientific decision-making. Yet its understanding in philosophical studies of science deserves renewed attention: Should philosophers think differently about the advancement of science when they deal with the uncertainty of outcome in ongoing research in comparison with historical episodes? This paper argues that normative appeals to empirical success in the evaluation of competing scientific explanations can result in unreliable conclusions, especially when we are looking at the changeability of direction in ongoing investigations. The challenges (...) we encounter arise from the inherent dynamics of disciplinary and experimental objectives in research practice. In this paper we discuss how these dynamics inform the evaluation of empirical success by analyzing three of its requirements: data accommodation, instrumental reliability, and predictive power. We conclude that the assessment of empirical success in developing inquiry is set against the background of a model’s interactive success and prospective value in an experimental context. Our argument is exemplified by the analysis of an apparent controversy surrounding the model of a quantum nose in research on olfaction. Notably the public narrative of this controversy rests on a distorted perspective on measures of empirical success. (shrink)

Ludwik Fleck, Edmund Husserl : on the historicity of scientific knowledge -- Gaston Bachelard : the concept of "phenomenotechnique" -- Georges Canguilhem : epistemological history -- Pisum : Carl Correns's experiments on Xenia, 1896-99 -- Eudorina : Max Hartmann's experiments on biological regulation in protozoa, 1914-21 -- Ephestia : Alfred Kähn's experimental design for a developmental physiological -- Genetics, 1924-45 -- Tobacco mosaic virus : virus research at the Kaiser Wilhelm Institutes for Biochemistry and Biology, 1937-45 -- The concept (...) of the gene : molecular biological perspectives -- The liquid scintillation counter : traces of radioactivity -- The concept of information : the writings of François Jacob -- Intersections -- Preparations -- The economy of the scribble. (shrink)

The short monograph Creative Nature is a welcome contribution to the philosophy of nature that arose from interdisciplinary conversations between authors who are both up-to-date in the scientific literature and deeply grounded in the western intellectual tradition. The authors draw from modern physics, biochemistry, evolutionary biology, developmental biology and ecology to argue that nature is creative in the sense that an “open future” of our evolving world lies ahead. In this review essay, divided into three parts, we offer (...) a chapter-by-chapter summary covering Nature, Life, Change, Limits, Functions and Creativity. In conclusion, we offer some pedagogical possibilities. The second part proposes certain points for deeper reflection. (shrink)

I consider some hitherto unexplored examples of teleological language in the sciences. In explicating these examples, I aim to show (a) that such language is not the sole preserve of the biological sciences, and (b) that not all such talk is reducible to the ascription of functions. In chemistry and biochemistry, scientists explaining molecular rearrangements and protein folding talk informally of molecules rearranging “in order to” maximize stability. Evolutionary biologists, meanwhile, often speak of traits evolving “in order to” optimize (...) some fitness-relevant variable. I argue that in all three contexts such locutions are best interpreted as shorthands for more detailed explanations which, were we to spell them out in full, would show that the relevant process would robustly converge towards the same end-point despite variation in initial conditions. This suggests that, in biology, such talk presupposes a substantial form of adaptationism. The upshot is that such shorthands may be more applicable in the physical sciences than the biological. (shrink)