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)

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

Review essay of The Philosophy of Experimental Biology by Marcel Weber (Cambridge University Press, 2005).

Historians of biology have argued that much of the dynamics of experimental disciplines such as genetics or molecular biology can be understood from studying experimental systems and model organisms alone . Such accounts contrast sharply with more traditional philosophies of science which viewed scientific research essentially as a process of inventing and testing theories. I present a case from the history of biochemistry which can be viewed from both the experimental systems perspective and from the (...) methodology of theory testing. I argue that not only are the two perspectives fully compatible, but they are both necessary for a complete account of the research process. (shrink)

El objetivo de este trabajo es poner al descubierto los principales valores cognitivos y epistemológicos desde los que Warren Weaver puso en marcha el Programa de Biología Experimental, un programa que llevado a cabo desde la presidencia de la división de ciencias naturales de la Fundación Rockefeller, marcó y condicionó en buena medida el posterior desarrollo de la investigación biológica. Para tal fin se mostrará, en primer lugar, cómo fue la llegada de Weaver a la Fundación Rockefeller, así como (...) las razones bajo las cuáles el consejo de esa institución decidió entre 1932 y 1933 dar prioridad a las investigaciones biomédicas, y la manera por la cual lo hicieron. En un segundo momento, el más extenso e importante, veremos algunos de los elementos más significativos de la perspectiva epistemológica y cognoscitiva de de Weaver. Finalizaremos viendo cómo esa perspectiva, desarrollada en conexión con el Programa de Biología Experimental, inter-actuó con la visión reduccionista de la biología a la que el programa parecía apuntar. The aim of this article is to uncover the main cognitive and epistemological values that influenced Warren Weaver in starting the Experimental Biology Program, a program carried out from the time that he became president of the Natural Sciences Division of the Rockefeller Foundation, and which significantly marked and conditioned the subsequent development of biological research. To this end, we first describe the arrival of Warren Weaver at the Rockefeller Foundation, and the reasons for which the Board of this Foundation, between 1932 and 1933, decided to prioritize biomedical research, and the manner in which they did so. Then, secondly, in the largest and most important part of the article, we will present some of the most significant elements of Weaver's epistemological and cognitive perspective. Finally, we will show how this perspective, developed in connection with the Experimental Biology Program, interacted with the reductionist view of biology to which the program seemed to point. (shrink)

Review\n\n"This bookas lucid, comprehensive presentation will enlighten both\nstudents and academicians in philosophy, biology, and science history,\nas well as scientists in other disciplines, while stimulating further\ndiscussion and analytical treatments." CHOICE May 2005 \n\n\n"Weber's overall approach is compelling; his book's focus on philosophical\nsignificance to be found in details of experimental biology is a\nwelcome addition to the philosophy of biology and to the philosophy\nof science more generally." - Jonathan Kaplan, Oregon State University\n\n\nProduct Description\n\nExploring central philosophical issues concerning scientific research\nin (...) modern experimental biology, this book clarifies the strategies,\nconcepts, reasoning, approaches, tools, models and experimental systems\ndeployed by researchers. It also integrates recent developments in\nhistorical scholarship, in particular, the New Experimentalism, making\nthis work of interest to philosophers and historians of science as\nwell as to biological researchers. (shrink)

Incommensurability of scientific theories, as conceived by Thomas Kuhnand Paul Feyerabend, is thought to be a major or even insurmountable obstacletothe empirical comparison of these theories. I examine this problem in light ofaconcrete case from the history of experimental biology, namely the oxidativephosphorylation controversy in biochemistry (ca. 1961-1977). After a briefhistorical exposition, I show that the two main competing theories which werethe subject of the ox-phos controversy instantiate some of the characteristicfeatures of incommensurable theories, namely translation failure,non-corresponding predictions, (...) and different claims about what kinds ofentitiesexist in the world. By examining how the controversy was eventually resolved, Ithen show that at least this pair of incommensurable theories couldneverthelessbe empirically compared. (shrink)

For over 20 years, the Schmid Training Course (STC) has offered unique opportunities for marine biology students from European universities to learn about marine model organisms. While the topics of the course have continuously changed over the years with the advent of new research techniques and discoveries, the pedagogical approach has remained largely the same – a combination of lectures, lab practicals, and field excursions. Several life science researchers, who have taught in the STC for many years, sought to (...) bring the course's pedagogical approach into the 21st century, and with the support of Erasmus+ Programme of the European Community funding, the Digital Marine project was developed. Digital Marine began in 2018 as an international partnership between the six research centers from which the STC instructors hail, and its main objective was to introduce a flipped, blended approach to learning and teaching with respect to established and emerging marine biological model systems. The Digital Marine platform, which covers 12 marine model organisms, is now publicly available. (shrink)

Diatoms are a species‐rich group of photosynthetic eukaryotes, with enormous ecological significance and great potential for biotechnology. During the last decade, diatoms have begun to be studied intensively using modern molecular techniques and the genomes of four diatoms have been wholly or partially sequenced. Although new insights into the biology and evolution of diatoms are accumulating rapidly due to the availability of reverse genetic tools, the full potential of these molecular biological approaches can only be fully realized if (...) class='Hi'>experimental control of sexual crosses becomes firmly established and widely accessible to experimental biologists. Here we discuss the issue of choosing new models for diatom research, by taking into account the broader context of diatom mating systems and the place of sex in relation to the intricate cycle of cell size reduction and restitution that is characteristic of most diatoms. We illustrate the results of our efforts to select and develop experimental systems in diatoms, using species with typical life cycle attributes, which could be used as future model organisms to complement existing ones. BioEssays 30:692–702, 2008. © 2008 Wiley Periodicals, Inc. (shrink)

Nach einer allgemeinen Diskussion des Zusammenhanges zwischen theoretischer und experimenteller Forschung, wird in Hinblick auf die vom Verfasser entwickelten physikalisch-mathematischen Grundlagen der Biologie, eine Reihe von Einzelproblemen betrachtet. Es wird an Hand von Kurvenmaterial gezeigt wie weit die mathematisch vorausgesagten Beziehungen mit den experimentellen Befunden übereinstimmen. Folgende Fragen werden besprochen: Zellatmung, Zellgrössen, deren Abhängigkeit von Stoffwechsel, Zellteilung, Protoplasmaströmungen, Nervenerregung, psychophysische Gesetze, Reaktion auf geometrische Gestalten.Après une mise au point générale de la relation entre les sciences théoriques et expérimentales, diverses questions (...) sont discutées, du point de vue des fondations physico-mathématiques de la biologie, développées récemment par l'auteur. On montre par la comparaison des courbes calculées à celles observées, comment les relations prédites mathématiquement se trouvent vérifiées. Les questions suivantes sont discutées: respiration cellulaire, dimensions cellulaires et leur rapport au métabolisme, division cellulaire, mouvements protoplasmiques, excitation nerveuse, les lois psychophysiques, perception des formes géométriques. (shrink)

Experimental modeling in biology involves the use of living organisms (not necessarily so-called "model organisms") in order to model or simulate biological processes. I argue here that experimental modeling is a bona fide form of scientific modeling that plays an epistemic role that is distinct from that of ordinary biological experiments. What distinguishes them from ordinary experiments is that they use what I call "in vivo representations" where one kind of causal process is used to stand in (...) for a physically different kind of process. I discuss the advantages of this approach in the context of evolutionary biology. (shrink)

In this paper I argue that we can best make sense of the practice of experimental evolutionary biology if we see it as investigating contingent, rather than lawlike, regularities. This understanding is contrasted with the experimental practice of certain areas of physics. However, this presents a problem for those who accept the Logical Positivist conception of law and its essential role in scientific explanation. I address this problem by arguing that the contingent regularities of evolutionary biology (...) have a limited range of nomic necessity and a limited range of explanatory power even though they lack the unlimited projectibility that has been seen by some as a hallmark of scientific laws. (shrink)

My paper draws on examples from molecular biology, the details of which I have developed elsewhere (Rheinberger 1992, 1993, 1995, 1997). Here, I can give only a brief outline of my argument. Reduction of complexity is a prerequisite for experimental research. To make sense of the universe of living beings, the modern biologist is bound to divide his world into fragments in which parameters can be defined, quantities measured, qualities identified. Such is the nature of any "experimental (...) system." Ontic complexity has to be reduced in order to make experimental research possible. The complexity of the research object, however, is epistemically retained in the rich context of an experimental landscape, where the eruption of "volcanic systems" can change the scenery dramatically as the result of particular, unprecedented findings. (shrink)

Since the 1940s, microbiologists, biochemists and population geneticists have experimented with the genetic mechanisms of microorganisms in order to investigate evolutionary processes. These evolutionary studies of bacteria and other microorganisms gained some recognition from the standard-bearers of the modern synthesis of evolutionary biology, especially Theodosius Dobzhansky and Ledyard Stebbins. A further period of post-synthesis bacterial evolutionary research occurred between the 1950s and 1980s. These experimental analyses focused on the evolution of population and genetic structure, the adaptive gain of (...) new functions, and the evolutionary consequences of competition dynamics. This large body of research aimed to make evolutionary theory testable and predictive, by giving it mechanistic underpinnings. Although evolutionary microbiologists promoted bacterial experiments as methodologically advantageous and a source of general insight into evolution, they also acknowledged the biological differences of bacteria. My historical overview concludes with reflections on what bacterial evolutionary research achieved in this period, and its implications for the still-developing modern synthesis. (shrink)

This paper examines two parallel discussions of scientific modeling which have invoked experimentation in addressing the role of models in scientific inquiry. One side discusses the experimental character of models, whereas the other focuses on their exploratory uses. Although both relate modeling to experimentation, they do so differently. The former has considered the similarities and differences between models and experiments, addressing, in particular, the epistemic value of materiality. By contrast, the focus on exploratory modeling has highlighted the various kinds (...) of exploratory functions of models in the early stages of inquiry. These two perspectives on modeling are discussed through a case study in the field of synthetic biology. The research practice in question explores biological control by making use of an ensemble of different epistemic means: mathematical models and simulations, synthetic genetic circuits and intracellular measuring devices, and finally electronic circuits. We argue that the study of exploratory modeling should trace the ways different epistemic means, in different materialities, are being combined over time. Finally, the epistemic status of such novel investigative objects as synthetic genetic circuits is evaluated, with the conclusion that they can function as both experiments and models. (shrink)

Organisms and other biological entities are mistake-prone: they get things wrong. The entities of pure physics, such as atoms and inorganic molecules, do not make mistakes: they do what they do according to physical law, with no room for error except on the part of the physicist or their theory. We set out a novel framework for understanding biology and its demarcation from physics – that of mistake-making. We distinguish biological mistakes from mere failures. We then propose a rigorous (...) definition of mistakes that, although invoking the concept of function, is compatible with various views about what functions are. The definition of mistake-making is agential, since mistakes do not just happen ¬– at least in the sense analysed here – but are made. This requires, then, a notion of biological agency which we set out as a definition of the Minimal Biological Agent. The paper then considers a series of objections to the theory presented here, along with our replies. Two key features of our theory of mistakes are, first, that it is a supplement to, not a replacement for, existing general frameworks within which biology is understood and practised. Secondly, it is designed to be experimentally productive. Hence we end with a series of case studies where mistake theory can be shown to be useful in the potential generation of research questions and novel hypotheses of interest to the working biologist. (shrink)

I use a recent ‘experimental philosophy’ study of the concept of the gene conducted by myself and collaborators to discuss the broader epistemological framework within which that research was conducted, and to reflect on the relationship between science, history and philosophy of science, and society.Keywords: Experimental philosophy; Biohumanities; Representing Genes Project; Gene concept; Science criticism; Conceptual ecology.

This paper aims to bring the epistemic dimensions of stem cell experiments out of the background, and show that they can be critically evaluated. After introducing some basic concepts of stem cell biology, I set out the current “gold standard” for experimental success in that field (§2). I then trace the origin of this standard to a 1988 controversy over blood stem cells (§3). Understanding the outcome of this controversy requires attention to the details of experimental techniques, (...) the organization of epistemic communities, and relations between the two (§4). With its resolution, a standard for experimental success was established for HSC research, which in turn serves as an exemplar for studies of other stem cells. This historical case study reveals a robust standard for experimental success in stem cell biology: to trace processes of development at the single-cell level, in the form of cell lineage hierarchies. Experiments conforming to this standard can be further critically assessed as means to the therapeutic end of stem cell research: use of stem cells to repair human organs and tissues. (shrink)

A clausura causal do domínio físico pode ser aceita sem por isso negarmos que exista genuíno conhecimento causal, capaz de nos habilitar ao controle experimental dos fenômenos, que não esteja formulado em termos físicos, e que dificilmente possa ser formulado nesses termos. A Biologia dá bons exemplos disso: tal é o caso das explicações que articuladas na base da Teoria da Seleção Natural; mas também é o caso das explicações fisiológicas. Elas, conforme Claude Bernard soube mostrá-lo, podem fornecer efetivo (...) e eficaz conhecimento causal, sem para isso ter que estar construídas em termos físico-químicos.: The causal closure of the physical domain can be accepted without denying that there exists genuine causal knowledge that can enable us to control experimental phenomena, but is not formulated in physical terms, and that can hardly be formulated in such terms. Biology gives good examples of it: such is the case of explanations articulated by Natural Selection Theory; but it is also the case of physiological explanations. These, as Claude Bernard could show, can provide effective and efficient causal knowledge without been constructed in physico -chemical terms. Keywords: Bernard, Claude; causal explanation; physicalism; reductionism; supervenience. (shrink)

According to the so-called Quantum Darwinist approach, the emergence of "classical islands" from a quantum background is assumed to obey a (selection) principle of maximal information. We illustrate this idea by considering the coupling of two oscillators (modes). As our approach suggests that the classical limit could have emerged throughout a long and progressive Evolution mechanism, it is likely that primitive living organisms behave in a "more quantum", "less classical" way than more evolved ones. This brings us to seriously consider (...) the possibility to measure departures from classicality exhibited by biological systems. We describe an experimental proposal the aimed at revealing the presence of entanglement in the biophotonic radiation emitted by biological sources. (shrink)

According to the so-called Quantum Darwinist approach, the emergence of “classical islands” from a quantum background is assumed to obey a principle of maximal information. We illustrate this idea by considering the coupling of two oscillators. As our approach suggests that the classical limit could have emerged throughout a long and progressive Evolution mechanism, it is likely that primitive living organisms behave in a “more quantum”, “less classical” way than more evolved ones. This brings us to seriously consider the possibility (...) to measure departures from classicality exhibited by biological systems. We describe an experimental proposal the aimed at revealing the presence of entanglement in the biophotonic radiation emitted by biological sources. (shrink)

The question on how the diverse forms of cooperative behavior in humans and nonhuman animals could have evolved under the pressure of natural selection has been a challenge for evolutionary biology ever since Darwin himself. In this chapter, we briefly review and summarize results from the last 50 years of research on human and nonhuman cooperativeness from a theoretical (biology) and an experimental perspective (experimental economics). The first section presents six concepts from theoretical biology able (...) to explain a variety of forms of cooperativeness which evolved in many different species. These are kin selection, mutualism, reciprocity, green-beard altruism, costly signaling, and cultural group selection. These considerations are complemented by two short examples of evolved cooperative behavior, one from microbiology and one from ethology. The second main section focuses on recent experimental research on human cooperativeness. We present a brief review of factors known to impact individual human decision-making in social dilemmas, most prominently communication, punishment, reputation, and assortment. Our conclusion then draws attention to tasks for further research in this area. (shrink)

In this paper the relationship between phenomenology of perception and synthetic phenomenology is discussed. Synthetic phenomenology is presented on the basis of the issues in A.I. and Robotics that required to address the question of what enables artificial agents to have phenomenal access to the environment. Phenomenology of perception is construed as a theory with autonomous structure and domain, which can be embedded in a philosophical as well as a scientific theory. Two attempts at specifying the phenomenal content of artificial (...) agents are discussed. Concepts and experimental evidence on the independence of perception and the coordination of motion and appearances are set out to submit that phenomenology of perception makes a contribution to synthetic phenomenology. (shrink)

Asking and answering questions is the cornerstone of science yet formal training in understanding this key process is often overlooked. "Asking Questions in Biology" unpacks this crucial process of enquiry, from a biological perspective, at its various stages. It begins with an overview of scientific question-asking in general, before moving on to demonstrate how to derive hypotheses from unstructured observations. It then explains in the main sections of the book, how to use statistical tests as tools to analyse data (...) and answer those questions before, finally, showing the best practice in presenting scientific reports. As such, it is an indispensable companion to all students of biology, but particularly those enrolled in courses concerning experimental design; data analysis; hypothesis testing; research methods; or any practical project work. The late Chris Barnard was Professor of Animal Behaviour at Nottingham University. Francis Gilbert is Associate Professor of Ecology at Nottingham University. Peter McGregor isa Reader in Applied Zoologyat Cornwall College. ". (shrink)

I attempt to characterize the relationship of classical experimental embryology (CEE) and molecular developmental biology and compare it to the much-discussed case of classical genetics. These sciences are treated here as discovery practices rather than as definitive forms of knowledge. I first show that CEE had some causal knowledge and hence was able to answer specific why?-questions. A paradigm was provided by the case of eye induction, perhaps CEE’s greatest success. The case of the famous Spemann-Mangold organizer is (...) more difficult. I argue that before the advent of molecular biology, knowledge of its causal role in development was very limited. As a result, there was no functional definition of the concept of organizer. I argue that, like the classical gene concept, it is best viewed as an operational concept. This means that an account of reduction such as Kim’s functional reduction, which is still a mainstay in scientific metaphysics, cannot work in these cases. Nonetheless, again like in the classical gene case, the operational concepts of CEE played an important heuristic role in the discovery of molecules involved in morphogenesis and cell differentiation. This was made possible by what I call inter-level investigative practices. These are practices that combine experimental manipulations targeting two (or more) different levels. I conclude that the two sciences are more closely related via their experimental practices than by any inter-level explanatory relations. (shrink)

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

By 1900 most biologists accepted experimentation as appropriate for at least parts of biology. Some claimed experimentation as the best or only proper approach to biology, while others regarded it as an acceptable addition to existing methodologies. Different researchers defined experimentation in different ways, and they held different aspirations for their experimental programs. This paper explores three sets of ideas, represented respectively by the French in the 1870s, the Germans in the 1880s, and the Americans in the (...) 1890s. It examines what an experiment was thought to be, what experimentation was, and what the goals of experimentation were for each group, revealing suggestive differences. (shrink)