Microscale techniques have been applied to biological assays for nearly two decades, but haven't been widely integrated as common tools in biological laboratories. The significant differences between several physical phenomena at the microscale versus the macroscale have been exploited to provide a variety of new types of assays (such as gradient production or spatial cell patterning). However, the use of these devices by biologists seems to be limited by issues regarding biological validation, ease of use, and the limited available readouts (...) for assays done using microtechnology. Critical validation work has been done recently that highlights the current challenges for microfluidic methods and suggest ways in which future devices might be improved to better integrate with biological assays. With more validation and improved designs, microscale techniques hold immense promise as a platform to study aspects of cell biology that are not possible using current macroscale techniques. BioEssays 30:811–821, 2008. © 2008 Wiley Periodicals, Inc. (shrink)

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

Human articulated motion can be readily recognized robustly even from impoverished so-called point-light displays. Such sequence information is processed by separate visual processing channels recruiting different stages at low and intermediate levels of the cortical visual processing hierarchy. The different contributions that motion and form information make to form articulated, or biological, motion perception are still under investigation. Here we investigate experimentally whether and how specific spatio-temporal features, such as extrema in the motion energy or maximum limb expansion, indicated by (...) the lateral and longitudinal extension, constrain the formation of the representations of articulated body motion. In order to isolate the relevant stimulus properties we suggest a novel masking technique, which allows to selectively impair the ankle information of the body configuration while keeping the motion of the point-light locations intact. Our results provide evidence that maxima in feature channel representations, e.g., the lateral or longitudinal extension, define elemental features to specify key poses of biological motion patterns. These findings provide support for models which aim at automatically building visual representations for the cortical processing of articulated motion by identifying temporally localized events in a continuous input stream. (shrink)

The question whether research techniques are producing artifacts or data is often a crucial one for scientists. The potential for artifacts results from the fact that generating data often requires numerous procedures that are often brutal, poorly understood, and very sensitive to details of the procedure. Through a case-study of the introduction of electron microscopy as a tool for studying cells, I examine how scientists judge whether new techniques are introducing artifacts. Three factors seem to be most salient in their (...) judgments: determinateness of the results, consilience of different procedures, and ability of the results to fit into emerging theories. (shrink)

The aim of this book is to show how supramolecular complexity of cell organization can dramatically alter the functions of individual macromolecules within a cell. The emergence of new functions which appear as a consequence of supramolecular complexity, is explained in terms of physical chemistry. The book is interdisciplinary, at the border between cell biochemistry, physics and physical chemistry. This interdisciplinarity does not result in the use of physical techniques but from the use of physical concepts to study biological problems. (...) In the domain of complexity studies, most works are purely theoretical or based on computer simulation. The present book is partly theoretical, partly experimental and theory is always based on experimental results. Moreover, the book encompasses in a unified manner the dynamic aspects of many different biological fields ranging from dynamics to pattern emergence in a young embryo. The volume puts emphasis on dynamic physical studies of biological events. It also develops, in a unified perspective, this new interdisciplinary approach of various important problems of cell biology and chemistry, ranging from enzyme dynamics to pattern formation during embryo development, thus paving the way to what may become a central issue of future biology. (shrink)

ArgumentBiological drawings of newly described or revised species are expected to represent the type specimen with greatest possible accuracy. In taxonomic practice, illustrations assume the function of mobile representatives of relatively immobile specimens. In other words, such illustrations serve as “immutable mobiles” in the Latourian sense. However, the significance of drawing in the context of first descriptions goes far beyond that of illustration in the conventional sense. Not only does it synthesize the verbal catalogue of the type's morphological characteristics: it (...) also enables the examination of these traits. The efficacy of drawing is thus closely related to its power to direct and redirect observation; it is inextricably bound up with the act of making a drawing. Although the invariance of the “immutable mobiles” is a key virtue of the logistics of “paperwork,” the recovery of graphic knowledge requires a much stronger dynamic activity – a process of sequential processing that brings out differences by translating the phenomenon under examination into various modes of graphic representation. (shrink)

This short and highly accessible volume opens up the subject of the philosophy of biology to professionals and to students in both disciplines. The text covers briefly and clearly all of the pertinent topics in the subject, dealing with both human and non-human issues, and quite uniquely surveying not only scholars in the English-speaking world but others elsewhere, including the Eastern block. As molecular biologists peer ever more deeply into life’s mysteries, there are those who fear that such ‘reductionism’ (...) conceals more than it reveals, and there are those who complain that the new techniques threaten the physical safety of us all. As students of evolution apply their new-found understanding to our own species, some people think that this is merely an excuse for racist and sexist propaganda, and others worry that the whole exercise blatantly violates the religious beliefs many of us hold dear. These controversies are the joint concern of biologists and philosophers—of those whose task it is to study the theoretical and moral foundations of knowledge. The comprehensive and fully up-to-date bibliography makes this an invaluable and indispensable guide. (shrink)

In biology proteins are uniquely important. They are not to be classed with polysaccharides, for example, which by comparison play a very minor role. Their nearest rivals are the nucleic acids....The main function of proteins is to act as enzymes....In the protein molecule Nature has devised a unique instrument in which an underlying simplicity is used to express great subtlety and versatility; it is impossible to see molecular biology in proper perspective until this peculiar combination of virtues has (...) been clearly grasped. (shrink)

The majority of biomedical and biological research relies on a few molecular biology techniques. Here we show that eight key molecular biology techniques would not exist without basic biological research.We also find that the scientific reward system does not sufficiently value basic biological research into molecular mechanisms.

Avec l’identification biométrique, nous passons imperceptiblement du contrôle à distance des populations pratiqué par les États modernes à des macro-systèmes techniques qui imposent de plus en plus leur propre logique. Du point de vue anthropologique ce déplacement de paradigme met en jeu la définition même de l’identité en renforçant le divorce entre l’identité civile et l’identité personnelle ou sociale. La frontière est désormais inscrite à même le corps biologique des individus au sein de l’espace géré depuis les terminaux du grand (...) réseau mondial de gestion des flux disséminés sur la planète. Elle tend donc à se confondre avec les limites fonctionnelles du Macro-Système technique. Du point de vue du droit, la mise en place par les États de dispositifs d’identification biométriques s’exprime principalement par la restriction de la liberté de circuler accordée aux individus. L’un des constats apporté par la revue des législations nationales montre pourtant que le droit s’adapte globalement à cette nouvelle situation. Cet article interroge en conclusion quelques-unes des raisons permettant d’expliquer ces reculs successifs et propose, parmi elles, la définition implicite de l’individu sur laquelle fait fond le droit moderne.With biometric identification we are imperceptibly moving from the remote control of the population practised by the modern States on to large technical systems which increasingly impose their own logic on people. From an anthropological viewpoint, this paradigm shift calls into question the very definition of « identity » by broadening the divide between civil identity and personal or social identity. The frontier is now inscribed on the biological body of the individual within the space that is managed from the terminals of the global flow management networks scattered the world over. The frontier thus tends increasingly to coincide with the functional limits of the large technical system. From a legal viewpoint, the introduction by States of biometric identification systems results primarily in a restriction of the freedom of circulation granted to individuals. One of the findings which emerge from a review of national legislations is however that law is globally adapting to this new situation. In the conclusion, the article considers some of the reasons behind these successive backward steps, and proposes, amongst them, an implicit definition of the individual on which modern law is founded. (shrink)

Scientific risk evaluations are constructed by specific evidence, value judgements and biological background assumptions. The latter are the framework-setting suppositions we apply in order to understand some new phenomenon. That background assumptions co-determine choice of methodology, data interpretation, and choice of relevant evidence is an uncontroversial claim in modern basic science. Furthermore, it is commonly accepted that, unless explicated, disagreements in background assumptions can lead to misunderstanding as well as miscommunication. Here, we extend the discussion on background assumptions from basic (...) science to the debate over genetically modified (GM) plants risk assessment. In this realm, while the different political, social and economic values are often mentioned, the identity and role of background assumptions at play are rarely examined. We use an example from the debate over risk assessment of stacked genetically modified plants (GM stacks), obtained by applying conventional breeding techniques to GM plants. There are two main regulatory practices of GM stacks: (i) regulate as conventional hybrids and (ii) regulate as new GM plants. We analyzed eight papers representative of these positions and found that, in all cases, additional premises are needed to reach the stated conclusions. We suggest that these premises play the role of biological background assumptions and argue that the most effective way toward a unified framework for risk analysis and regulation of GM stacks is by explicating and examining the biological background assumptions of each position. Once explicated, it is possible to either evaluate which background assumptions best reflect contemporary biological knowledge, or to apply Douglas' 'inductive risk' argument. (shrink)

In the first decades of the twentieth century, the process of photosynthesis was still a mystery: Plant scientists were able to measure what entered and left a plant, but little was known about the intermediate biochemical and biophysical processes that took place. This state of affairs started to change between the two world wars, when a number of young scientists in Europe and the United States, all of whom identified with the methods and goals of physicochemical biology, selected photosynthesis (...) as a topic of research. The protagonists had much in common: They had studied physics and chemistry (although not necessarily plant physiology) to a high level; they used physicochemical methods to study the basic processes of life; they believed these processes were the same, or very similar, in all life forms; and they were affiliated with institutions that fostered this kind of study. This set of cognitive, methodological, and material resources enabled these protagonists to transfer their knowledge of the concepts and techniques from microbiology and human biochemistry, for example, to the study of plant metabolism. These transfers of knowledge had a great influence on the way in which the biochemistry and biophysics of photosynthesis would be studied over the following decades. Through the use of four historical cases, this paper analyzes these knowledge transfers, as well as the investigative pathways that made them possible. (shrink)

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

[ENGLISH] This article discusses the potential of synthetic biology to address fundamental questions in the philosophy of biology regarding the nature of life and biological functions. Synthetic biology aims to reduce living organisms to their simplest forms by identifying the minimal components of a cell and also to create novel life forms through genetic reprogramming, biobrick assembly, or novel proteins. However, the technical success of these endeavors does not guarantee their conceptual success in defining life. There is (...) a lack of consensus among researchers on how to define and classify the entities produced in the lab, whether they should be considered living or categorized differently. The criteria for minimal cells and minimal life are subject to arbitrary choices and varying interpretations. The concept of function, crucial to synthetic biology, is also difficult to define. The article highlights the need to consider the minimal set of functions that characterize life before determining the smallest genomes that code for those functions. The arbitrary nature of defining both life and function complicates the understanding and classification of these entities. The article suggests that the traditional dichotomy between the living and the non-living may no longer be valid and that the concept of life itself may not require precise scientific definition. As synthetic biology advances, the article emphasizes the importance of redefining or constructing new categories to encompass the expanding possibilities and creations in the field. The ability to create new life forms raises questions about recognition, identification, and ethical implications, requiring a conceptual and philosophical engagement beyond the technical achievements of synthetic biology. -/- [FRENCH] L'article aborde le potentiel de la biologie synthétique pour répondre à des questions fondamentales de la philosophie de la biologie concernant la nature de la vie et des fonctions biologiques. La biologie synthétique vise à réduire les organismes vivants à leurs formes les plus simples en identifiant les composants minimaux d'une cellule et à créer de nouvelles formes de vie grâce à la reprogrammation génétique, à l'assemblage de biobriques ou à des protéines nouvelles. Cependant, le succès technique de ces approches ne garantit pas leur réussite conceptuelle dans la définition de la vie. Il n'y a pas de consensus parmi les chercheurs sur la façon de définir et de classer les entités produites en laboratoire, qu'elles doivent être considérées comme vivantes ou catégorisées différemment. Les critères des cellules minimales et de la vie minimale sont soumis à des choix arbitraires et à des interprétations variables. La notion de fonction, essentielle en biologie synthétique, est également difficile à définir. L'article met en évidence la nécessité de prendre en compte l'ensemble minimal de fonctions qui caractérisent la vie avant de déterminer les plus petits génomes qui codent ces fonctions. La nature arbitraire de la définition de la vie et de la fonction complique la compréhension et la classification de ces entités. L'article suggère que la dichotomie traditionnelle entre le vivant et le non-vivant pourrait ne plus être valable et que le concept même de vie ne nécessite pas une définition scientifique précise. À mesure que la biologie synthétique progresse, l'article souligne l'importance de redéfinir ou de construire de nouvelles catégories pour englober les possibilités et créations croissantes dans le domaine. La capacité à créer de nouvelles formes de vie soulève des questions de reconnaissance, d'identification et d'implications éthiques, nécessitant une réflexion conceptuelle et philosophique au-delà des avancées techniques de la biologie synthétique. (shrink)

Molecular systems orchestrating the biology of the cell typically involve a complex web of interactions among various components and span a vast range of spatial and temporal scales. Computational methods have advanced our understanding of the behavior of molecular systems by enabling us to test assumptions and hypotheses, explore the effect of different parameters on the outcome, and eventually guide experiments. While several different mathematical and computational methods are developed to study molecular systems at different spatiotemporal scales, there is (...) still a need for methods that bridge the gap between spatially‐detailed and computationally‐efficient approaches. In this review, we summarize the capabilities of agent‐based modeling (ABM) as an emerging molecular systems biology technique that provides researchers with a new tool in exploring the dynamics of molecular systems/pathways in health and disease. (shrink)

History and Philosophy of Biology summarizes the major philosophical ideas that have attended the development of science in general and of biology in particular. The book then explores how the techniques and the concepts of the physical sciences have impacted biology. A reductionist approach to biology -- anatomy, physiology, genetics -- complements the study of evolution by natural selection and an ecological perspective. The final section of the book explores several examples of the influence of science (...) on society, and of society on science. Each of 46 chapters of History and Philosophy of Biology has been or could be the topic of a major tome. The book is unique in that it explores the web of interactions among issues of philosophy, techniques and concepts of the physical sciences, fields of biology, and the diverse relationships between society and science. The book should appeal to readers of Scientific American or the New York Review of Books even if they are not trained biologists. It is a good text, or additional reading, for an advanced undergraduate course treating history and/or philosophy of biology or of science in general. (shrink)

A crucial part of the knowledge of molecular biologists is procedural knowledge, that is, knowledge of how to do things in laboratories. Procedural knowledge of molecular biologists involves both perceptual-motor skills and cognitive skills. We discuss such skills required in performing the most commonly used molecular biology techniques, namely, Polymerase Chain Reaction and gel electrophoresis. We argue that procedural knowledge involved in performing these techniques is more than just knowing their protocols. Creative exploration and experience are essential for the (...) acquisition of procedural knowledge in molecular biology. With enough experience, molecular biologists make intuitive judgments without recourse to analytical reasoning. We propose that procedural knowledge is intuitive recognition of the patterns of one's environment that are the most relevant for making a decision or acting appropriately. Finally, we argue that knowledge of molecular biologists requires an integration of procedural knowledge and propositional knowledge. (shrink)

In the last few years, biologists and computer scientists have claimed that the introduction of data science techniques in molecular biology has changed the characteristics and the aims of typical outputs (i.e. models) of such a discipline. In this paper we will critically examine this claim. First, we identify the received view on models and their aims in molecular biology. Models in molecular biology are mechanistic and explanatory. Next, we identify the scope and aims of data science (...) (machine learning in particular). These lie mainly in the creation of predictive models which performances increase as data set increases. Next, we will identify a tradeoff between predictive and explanatory performances by comparing the features of mechanistic and predictive models. Finally, we show how this a priori analysis of machine learning and mechanistic research applies to actual biological practice. This will be done by analyzing the publications of a consortium—The Cancer Genome Atlas—which stands at the forefront in integrating data science and molecular biology. The result will be that biologists have to deal with the tradeoff between explaining and predicting that we have identified, and hence the explanatory force of the ‘new’ biology is substantially diminished if compared to the ‘old’ biology. However, this aspect also emphasizes the existence of other research goals which make predictive force independent from explanation. (shrink)

This article revisits French sociologist Marcel Mauss’ notion of ‘techniques of the body’ to analyze the emergence of corporeal and behavioral norms instituted to prevent the spread of the coronavirus pandemic. Centering its analysis on the early stages of COVID’s global spread, the article examines a range of everyday, micro-practices that reveal how the pandemic changed our awareness, uses, and assessments of our own and others’ bodies. In a context where to not touch was to care, people often struggled to (...) find a balance between maintaining social civility and sustaining collective health. Failure to adapt the body to pandemic conditions, or instances of COVID faux-pas, resulted in discomfort, embarrassment, or annoyance on the part of those who perceived this behavior as irresponsible, dangerous, and selfish. Changing bodily practices thus became subject to judgment in ways that sometimes obscured the uneven distribution of risk and protection afforded to differently privileged or vulnerable human communities as they grappled with the uncertain phenomenologies of pandemic living and dying. COVID-19 corporealities, both fleshly and virtual, thus reveal the conjoined articulation of the social, biological, cultural, moral, and psychological in our bodily movements, expressions, and assessments. In contrast to Mauss’ theorization, many techniques of the body in the Covidscape were experienced as new, contextual, shifting, and improvised. They spoke to necessity and challenge of articulating a different relationship to the world and to others, enacted in the minute and mundane practices of everyday life, through which macro-level processes and forces are embodied and evaluated. (shrink)

Over the last decade the modeling and the storage of biological data has been a topic of wide interest for scientists dealing with biological and biomedical research. Currently most data is still stored in text files which leads to data redundancies and file chaos.In this paper we show how to use relational modeling techniques and relational database technology for modeling and storing biological sequence data, i.e. for data maintained in collections like EMBL or SWISS-PROT to better serve the needs for (...) these application domains.For this reason we propose a two step approach. First, we model the structure (and therefore the meaning of the) data using an Entity-Relationship approach. The ER model leads to a clean design of a relational database schema for storing and retrieving the DNA and protein data extracted from various sources. Our approach provides the clean basis for building complex biological applications that are more amenable to changes and software ports than their file-base counterparts. (shrink)

Many historical studies tend to underline two central Kantian themes frequently emerging in Georges Canguilhem’s works: (1) a conception of activity, primarily stemming from the Critique of Pure Reason, as a mental and abstract synthesis of judgment; and (2) a notion of organism, inspired by the Critique of Judgment, as an integral totality of parts. Canguilhem was particularly faithful to the first theme from the 1920s to the first half of the 1930s, whereas the second theme became important in the (...) early 1940s. With this article, I will attempt to show that a third important theme of technique arose in the second half of the 30s also in the wake of Kant’s philosophy, especially Sect. 43 of the Critique of Judgment. This section, which states that technical ability is distinguished from a theoretical faculty, led Canguilhem to a more concrete and practical conception of activity. I will then suggest that it was by considering technique that the concept of normativity, which characterizes Georges Canguilhem’s philosophy of life, also took shape. (shrink)

In the last few years, biologists and computer scientists have claimed that the introduction of data science techniques in molecular biology has changed the characteristics and the aims of typical outputs (i.e. models) of such a discipline. In this paper we will critically examine this claim. First, we identify the received view on models and their aims in molecular biology. Models in molecular biology are mechanistic and explanatory. Next, we identify the scope and aims of data science (...) (machine learning in particular). These lie mainly in the creation of predictive models which performances increase as data set increases. Next, we will identify a tradeoff between predictive and explanatory performances by comparing the features of mechanistic and predictive models. Finally, we show how this a priori analysis of machine learning and mechanistic research applies to actual biological practice. This will be done by analyzing the publications of a consortium—The Cancer Genome Atlas—which stands at the forefront in integrating data science and molecular biology. The result will be that biologists have to deal with the tradeoff between explaining and predicting that we have identified, and hence the explanatory force of the ‘new’ biology is substantially diminished if compared to the ‘old’ biology. However, this aspect also emphasizes the existence of other research goals which make predictive force independent from explanation. (shrink)

Structural biology has experienced several transformative technological advances in recent years. These include: development of extremely bright X-ray sources and the use of electrons to extend protein crystallography to ever decreasing crystal sizes; and an increase in the resolution attainable by cryo-electron microscopy. Here we discuss the use of these techniques in general terms and highlight their application for biological filament systems, an area that is severely underrepresented in atomic resolution structures. We assemble a model of a capped tropomyosin-actin (...) minifilament to demonstrate the utility of combining structures determined by different techniques. Finally, we survey the methods that attempt to transform high resolution structural biology into more physiological environments, such as the cell. Together these techniques promise a compelling decade for structural biology and, more importantly, they will provide exciting discoveries in understanding the designs and purposes of biological machines. Structural biology is undergoing technological advancements that now reveal the structures of previously inaccessible biological machines. Microfocus synchrotron beamlines, X-ray free electron lasers, and MicroED cope with vanishingly small crystals, while cryo-electron microscopy targets single molecules at near atomic resolution. These advances promise an exciting decade for structural biology. (shrink)

We present techniques for integrating low‐level neurobiological constraints into high‐level, functional cognitive models. In particular, we use these techniques to construct a model of eyeblink conditioning in the cerebellum based on temporal representations in the recurrent Granule‐Golgi microcircuit.

Over the last decade the modeling and the storage of biological data has been a topic of wide interest for scientists dealing with biological and biomedical research. Currently most data is still stored in text files which leads to data redundancies and file chaos.In this paper we show how to use relational modeling techniques and relational database technology for modeling and storing biological sequence data, i.e. for data maintained in collections like EMBL or SWISS-PROT to better serve the needs for (...) these application domains. (shrink)

The timeliness of the problem of reduction is due above all to the successes of application of the techniques of the exact sciences in biology. To the extent that molecular biology "gets down to" the initial, fundamental mechanisms of the processes of life, it is impossible for it to remain purely in the realm of statement of facts; it cannot but affect methodological principles of the study of life. "The history of biology clearly demonstrates the striking regularity (...) with which the problem of reductionism arises each time biological knowledge advances to a new level." The counterposing of mechanism and vitalism, elementarism and organicism, etc., was replaced by new forms of methodological discussion born of the achievements of experimental knowledge of life and the demands that this be formulated into theory. To separate the principle of reduction, productive in current biological research, from biological reductionism based on the elevation of this principle to an absolute is the meaning of the current struggle against mechanistic trends in biology. The mechanicism of the present day rests primarily on the productiveness of the methods of physical chemistry in adding to knowledge of life; and therefore when people speak of the problem of reductionism, discussion of the potentials of the investigation of life by molecular biology and the limits of those potentials takes pride of place. (shrink)

Within feminist literature from the early 1970s to this day, assisted reproductive technologies have been largely known to divide, replace or eliminate biological motherhood. For example, while in the past biological motherhood was considered a continuous experience, in vitro fertilisation (IVF) and IVF using egg donation allowed a split between two biological mothers, one providing eggs (genetic mother) and the other one gestation (gestational mother). This split was considered irreparable: the genetic mother could not be also gestational, and vice versa. (...) On the contrary, this paper aims to show that assisted reproductive technologies may also have a constructive potential towards biological motherhood(s). To explain how it could be possible, two existing techniques are explored: the first is maternal spindle transfer, which allows a double genetic motherhood; the second is reciprocal effortless IVF, which supposedly enables a double gestational motherhood. While in the first part, these techniques are examined singularly, in the second part a feasible combination of them is speculated. The idea is that assisted reproductive technologies could ‘recombine’ genetic and gestational motherhood in two figures that include both, namely in two ‘complete’ biological mothers, both genetic and gestational. (shrink)

In February 2015 the UK became the first country to legalise high-profile mitochondrial replacement techniques, which involve the creation of offspring using genetic material from three individuals. The aim of these new cell reconstruction techniques is to prevent the transmission of maternally inherited mitochondrial disorders to biological offspring. During the UK debates, MRTs were often positioned as a straightforward and unique solution for the ‘eradication’ of mitochondrial disorders, enabling hundreds of women to have a healthy, biologically-related child. However, many questions (...) regarding future applications and potential users remain. Drawing on a current qualitative study on reproductive choices in the context of mitochondrial disorders, this article illustrates how the potential limitations of MRTs have been obscured in public debates by contrasting the claims made about the future beneficiaries with insights from families affected by mitochondrial disorders and medical experts. The analysis illuminates the complex choices with which families and individuals affected by mitochondrial disorders are faced, which have thus far remained invisible. An argument is presented for improved information for the public as well as an intensification of critical empirical research around the complex and specific needs of future beneficiaries of new reproductive biotechnologies. (shrink)

Continuous culture techniques were developed in the early twentieth century to replace cumbersome studies of cell growth in batch cultures. In contrast to batch cultures, they constituted an open concept, as cells are forced to proliferate by adding new medium while cell suspension is constantly removed. During the 1940s and 1950s new devices have been designed—called “automatic syringe mechanism,” “turbidostat,” “chemostat,” “bactogen,” and “microbial auxanometer”—which allowed increasingly accurate quantitative measurements of bacterial growth. With these devices cell growth came under the (...) external control of the experimenters and thus accessible for developing a mathematical theory of growth kinetics—developed mainly by Jacques Monod, Aron Novick and Leo Szilard in the early 1950s and still in use today. The paper explores the development of continuous culture devices and claims that these devices are simulators for standard cells following specific requirements, in particular involving mathematical constraints in the design and setting of the devices as well as experiments. These requirements have led to contemporary designs of continuous culture techniques realizing a specific event-based flow algorithm able to simulate directed evolution and produce artificial cells and microorganisms. This current development is seen as an alternative approach to today’s synthetic biology. (shrink)

Synthetic biology (synbio) involves designing and creating new living systems to serve human ends, using techniques including molecular biology, genomics, and engineering. Existing bioethical analyses of synbio focus largely on balancing benefits against harms, the dual-use dilemma, and metaphysical questions about creating and commercializing synthetic organisms. We argue that these approaches fail to consider key feminist concerns. We ground our normative claims in two case studies, focusing on the public good, who holds and wields power, and synbio research (...) projects’ particularity and context. Attention to feminist concerns is essential for synbio to realize its potential in ethically justifiable ways. (shrink)

In this paper, I investigate the variety and richness of the taxonomical practices between the end of the nineteenth and the early twentieth centuries. During these decades, zoologists and paleontologists came up with different quantitative practices in order to classify their data in line with the new biological principles introduced by Charles Darwin. Specifically, I will investigate Florentino Ameghino’s mathematization of mammalian dentition and the quantitative practices and visualizations of several German-speaking paleontologists at the beginning of the twentieth century. In (...) so doing, this paper will call attention to the visual and quantitative language of early twentieth-century systematics. My analysis will therefore contribute to a prehistory of the statistical frame of mind in biology, a study which has yet to be written in full. Second, my work highlights the productive intertwinement between biological practices and philosophical frameworks at the turn of the nineteenth century. Deeply rooted in Kantian bio-philosophy, several biologists sought to find rules in order to apply ordering principles to chaotic taxonomic information. This implies the necessity to investigate the neglected role of Kantian and Romantic bio-philosophy in the unfolding of twentieth-century biology. (shrink)

Mangroves and seagrasses form extensive and highly productive ecosystems that are both biologically diverse and economically valuable. This book, now in its third edition and fully updated throughout, continues to provide a current and comprehensive introduction to all aspects of the biology and ecology of mangroves and seagrasses. Using a global range of examples and case studies, it describes the unique adaptations of these plants to their exacting environments; the rich and diverse communities of organisms that depend on mangrove (...) forests and seagrass meadows ; the links between mangrove, seagrass, and other habitats; and the evolution, biodiversity, and biogeography of mangroves and seagrasses. The economic value of mangroves and seagrasses is also discussed, including approaches to rational management of these vital resources and techniques for the restoration of degraded habitats. A final chapter, new to this edition, examines the potential effects of global climate change including sea level rise.As with other titles in the Biology of Habitats Series, particular emphasis is placed on the organisms that dominate these fascinating aquatic ecosystems although pollution, conservation, and experimental aspects are also considered. This accessible textbook assumes no previous knowledge of mangrove or seagrass ecology and is intended for senior undergraduate and graduate students, as well as professional ecologists, conservation practitioners, and resource managers. (shrink)

Integrative systems biology is an emerging field that attempts to integrate computation, applied mathematics, engineering concepts and methods, and biological experimentation in order to model large-scale complex biochemical networks. The field is thus an important contemporary instance of an interdisciplinary approach to solving complex problems. Interdisciplinary science is a recent topic in the philosophy of science. Determining what is philosophically important and distinct about interdisciplinary practices requires detailed accounts of problem-solving practices that attempt to understand how specific practices address (...) the challenges and constraints of interdisciplinary research in different contexts. In this paper we draw from our 5-year empirical ethnographic study of two systems biology labs and their collaborations with experimental biologists to analyze a significant problem-solving approach in ISB, which we call adaptive problem solving. ISB lacks much of the methodological and theoretical resources usually found in disciplines in the natural sciences, such as methodological frameworks that prescribe reliable model-building processes. Researchers in our labs compensate for the lack of these and for the complexity of their problems by using a range of heuristics and experimenting with multiple methods and concepts from the background fields available to them. Using these resources researchers search out good techniques and practices for transforming intractable problems into potentially solvable ones. The relative freedom lab directors grant their researchers to explore methodological options and find good practices that suit their problems is not only a response to the complex interdisciplinary nature of the specific problem, but also provides the field itself with an opportunity to discover more general methodological approaches and develop theories of biological systems. Such developments in turn can help to establish the field as an identifiably distinct and successful approach to understanding biological systems. (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 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)

"By combining recent advances in the physical sciences with some of the novel ideas, techniques, and data of modern biology, this book attempts to achieve a new and different kind of evolutionary synthesis. I found it to be challenging, fascinating, infuriating, and provocative, but certainly not dull."--James H, Brown, University of New Mexico "This book is unquestionably mandatory reading not only for every living biologist but for generations of biologists to come."--Jack P. Hailman, Animal Behaviour , review of the (...) first edition "An important contribution to modern evolutionary thinking. It fortifies the place of Evolutionary Theory among the other well-established natural laws."--R.Gessink, TAXON. (shrink)

Despite the transformation in biological practice and theory brought about by discoveries in molecular biology, until recently philosophy of biology continued to focus on evolutionary biology. When the Human Genome Project got underway in the late 1980s and early 1990s, philosophers of biology -- unlike historians and social scientists -- had little to add to the debate. In this landmark collection of essays, Sahotra Sarkar broadens the scope of current discussions of the philosophy of biology, (...) viewing molecular biology as a unifying perspective on life that complements that of evolutionary biology. His focus is on molecular biology, but the overriding question behind these papers is what molecular biology contributes to all traditional areas of biological research.Molecular biology -- described with some foresight in a 1938 Rockefeller Foundation report as a branch of science in which "delicate modern techniques are being used to investigate ever more minute details" -- and its modeling strategies apparently argue in favor of physical reductionism. Sarkar's first three chapters explore reductionism -- defending it, but cautioning that reduction to molecular interactions is not necessarily a reduction to genetics. The next sections of the book discuss function, exploring how functional explanations pose a problem for reductionism; the informational interpretation of biology and how it interacts with reductionism; and the tension between the unifying framework of molecular biology and the received framework of evolutionary theory. The concluding chapter is an essay in the emerging field of developmental evolution, exploring what molecular biology may contribute to the transformation of evolutionary theory as evolutionary theory takes into account morphogenetic development. (shrink)

RésuméLe dosage de traces de molécules organiques dans les matrices biologiques fait appel à des techniques analytiques physico‐chimiques dont la chromatographie en phase gazeuse couplée à la spectrumétrie de masse est une des plus puissantes. Des possibilityés nouvelles pour augmenter la sensibilityé de la détection de ces substances sont presentees et mises en relation avec la signification physiologique des résultats obtenus.SummaryGas chromatography‐mass spectrometry is the method of choice for the quantitative determination of organic traces in biological systems. New technical developments (...) allow higher sensitivity and greater specificity which are discussed together with the physiological meaning of the data thus obtained.ZusammenfassungDie Dosierung der Spuren von organischen Molekülen in den biologischen Matrizen erfordert physico‐chemische analytische Techniken, deren Chromatographie in gasförmiger Phase ver‐bunden mit der Massenspektrometrie eine der mächtigsten ist. Es werden neue Möglichkeiten zur Steigerung der Empfindlichkeit der Aufweisung dieser Substanzen vorgelegt, und mit der physio‐logischen Bedeutung der erhaltenen Ergebnisse in Beziehung gesetzt. (shrink)

Although there is little empirical doubt of the cerebral base of consciousness, it still has an unapproachable quality about it. Gerald Edelman and Giulio Tononi offer a hypothesis that should give us the tool to start disentangling the 'world knot', an image Arthur Schopenhauer used to describe the problem of the origin of consciousness. Their primary focus is not the richness in everyday experience, but the conditions that allow us that experiential richness -- a difficult enough task, as most would (...) admit reading the book. It shows how the cranial barrier can be overcome by new observation techniques, producing a plethora of experimental data in support of the concepts and theories described in the book. This material leads to the formulation of the dynamic-core hypothesis which describes the necessary biological conditions for consciousness. (shrink)