Las aminas biógenas son compuestos nitrogenados de pequeño tamaño con actividad biológica que se forman por la descarboxilación enzimática de ciertos aminoácidos. Las aminas biógenas se encuentran presentes en todos los seres vivos, en los que participan en procesos biológicas de gran importancia. Sin em­bargo, debido al metabolismo de algunos microorganismos, estos compuestos se pueden acumular en alimentos en concentraciones elevadas, constituyendo un riesgo para la salud de los consumido­res. Para que las aminas biógenas alcancen estas concentraciones elevadas en los (...) alimentos se requiere, como condición indispensa­ble, la presencia de microrganismos productores, por lo que se han desarrollado diferentes métodos para detectar la presencia de los mismos. Entre estos métodos, aquellos basados en técnicas inde­pendientes de cultivo, como la PCR, presentan ventajas como su gran especificidad, el hecho de ser rápidos y de fácil realización, y que en muchos casos ni siquiera es necesario un tratamiento previo de la muestra, lo que facilita su incorporación a las plantas de elabo­ración. En este trabajo se describen algunos de los métodos dispo­nibles en la actualidad para la detección de microorganismos pro­ductores de aminas biógenas, así como sus posibles aplicaciones. (shrink)

The most interesting biological molecules are long polymers. In analogy with human alphabetic languages, they can be called texts and analysed, as to the primary structure, as sequences of letters or of words . It is considered that the study of words, in a linguistic approach, may contribute positively to the understanding of molecular interactions . The molecular and human languages and dialects are contrasted. The molecular one is peculiarly distinct from the human, for instance, by its use of a (...) tridimensional morphology, temporal dynamics, absence of spacings and punctuation, and overlapping messages. A mathematical method is presented, for discovering words in texts. The word AAA was studied in the evolution of the 5S ribosomal RNA. It was shown that this word is more frequent in less complex organisms and less frequent in the more complex ones, in the fungi, plants, and vertebrates lineages. In the two latter ones, the degree of genie variability was also reduced. To the contrary, a moderate degree of usage of this word persisted in the whole invertebrates lineage, where a high degree of genie variability was maintained. In mitochondria, plastids and mycoplasmas, the frequency of the word AAA was increased, consistently with their need for interactions with a wider range of variation. These behaviors indicate that the monotonous AAA word allows for ambiguity in interactions. With the evolution of organic complexity and of greater molecular specificity, ambiguous words were progressively avoided.As moléculas biológicas mais interessantes são longos polímeros. Em analogia com a linguagem humana alfabética, estes podem ser chamados de textos, e analisados, quanto à estrutura primária, como sequência de letras ou de palavras . Considera-se que o estudo das palavras, em abordagem de tipo lingüístico, possa contribuir para o entendimento das interações moleculares. As linguagens e dialetos, moleculares e humanos, são contrastados. A linguagem molecular se distingue peculiarmente da humana, por exemplo, por utilizar forma tridimensional, dinâmica temporal, ausência de espaçamento e pontuação, e sobreposição de significados. Apresenta-se um método matemático para descoberta, de palavras em textos. A palavra AAA foi estudada na evolução do RNA ribossômico 5S. Observou-se que esta palavra é mais freqüente em organismos menos complexos e menos freqüente nos mais complexos, das linhagens de fungos, plantas e vertebrados. Nas duas últimas, reduziu-se também o grau de variabilidade gênica. Pelo contrário, grau moderado de freqüência da palavra persistiu em toda a linhagem dos invertebrados, com manutenção paralela de alto nível de variabilidade gênica. Nas mitocôndrias, plastídeos e micoplasmas, a freqüência da palavra AAA foi aumentada, de acordo com sua necessidade de interações com maior amplitude de variação. Esses comportamentos indicam que a palavra monótona AAA permite ambigüidade de interações. Com a evolução da complexidade orgânica e da maior especificidade molecular, as palavras ambíguas foram progressivamente evitadas. (shrink)

Los principales patógenos víricos que podemos ad­quirir ingiriendo alimentos contaminados son los norovirus, el virus de la hepatitis A y el virus de la hepatitis E que se propagan principalmente a través de la vía fecal oral. En los últimos años, la incidencia de brotes de transmisión alimentaria causados por estos patógenos ha experimentado un aumento considerable, en parte debido al comercio globalizado y a los cambios en los hábitos de consumo. Las matrices alimentarias que mayor riesgo representan para el (...) consumidor son los moluscos bivalvos, ve­getales de IV gama, frutas tipo baya y platos listos para comer. Actualmente las técnicas moleculares son las más habituales para la detección de estos patógenos en alimentos, aunque toda­vía existen dudas acerca del significado de la presencia de estos genomas víricos en términos de seguridad alimentaria. La infec­tividad de estos patógenos en alimentos viene también determi­nada por su elevada persistencia ambiental y por su resistencia a los tratamientos aplicados para la conservación de los alimentos. (shrink)

To act or think like a thing is a theme that runs as a red thread through Sartre’s oeuvre, but it is only in his Critique of Dialectical Reason that he would come to a coherent account of reifcation, which underpins what is perhaps his most seminal achievement in this book, the theory of the series. In contrast to Lukács’ account of reification, which has roots in Marx’s notion of social form, Sartre’s theory draws on diferent theoretical resources, such as (...) the notion of inertia and the exteriorisation of internal relations. It underpins his notion of the mass, which he understands as fundamentally ambivalent: the mass is the product of seriality and reification, it is the subject of steering and manipulation, but it can never be fully controlled. In specifc circumstances its internal dynamic can lead to forms of dereification through the interiorisation of number, which underpins the formation of a group, the agent of collective action. (shrink)

The rapidly changing field of genetics affects society through advances in health-care and through implications of genetic research. This study addresses the impacts of new genetic discoveries and technologies on different segments of today's society. The book begins with a chapter on genetic complexity, and subsequent chapters discuss moral and ethical questions arising from today's genetics from the perspectives of health care professionals, the media, the general public, special interest groups and commercial interests.

This paper deals with the interrelationship between causal explanation and methodology in a relatively young discipline in biology: epigenetics. Based on cases from molecular and ecological epigenetics, I show that James Woodward’s interventionist account of causation captures essential features about how epigeneticists using highly diverse methods, i.e. laboratory experiments and purely observational studies, think about causal explanation. I argue that interventionism thus qualifies as a useful unifying explanatory approach when it comes to cross-methodological research efforts. It can act as a (...) guiding rationale (i) to link causal models in molecular biology with statistical models derived from observational data analysis and (ii) to identify test-criteria for reciprocal transparent studies in different fields of research, which is a shared issue across the sciences.Este artículo trata de la relación entre explicaciones causales y metodología en una disciplina biológica relativamente joven, la epigenética. Basándome en casos de la epigenética molecular y ecológica, muestro que la concepción intervencionista de la causalidad desarrollada por James Woodward capta algunos rasgos esenciales del modo en que los epigenetistas conciben la explicación causal usando métodos sumamente diversos: e.g., experimentos de laboratorio o estudios observacionales. Defiendo que el intervencionismo es útil como aproximación unificadora a la explicación cuando se trata de empresas investigadoras transdisciplinares. Puede servir como guía para (i) conectar los modelos causales en biología molecular con los modelos estadísticos derivados del análisis de datos observacionales y (ii) para identificar criterios de prueba para estudios recíprocos en diferentes ámbitos de investigación, un problema de interés común en diferentes ciencias. (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)

There is consensus within the chemosciences that olfactory perception is of the molecular structure of chemical compounds, yet within philosophical theories of smell there is little agreement about the nature of smell. The paper critically assesses the current state of debate regarding smells within philosophy in the hopes of setting it upon firm scientific footing. The theories to be covered are: Naïve Realism, Hedonic Theories, Process Theory, Odor Theories, and non-Objectivist Theories. The aforementioned theories will be evaluated based on their (...) explanations of the (a) the olfactory quality of a smell, (b) smells as distal entities, and (c) our experience of smells as intentional objects. The paper concludes with a defense of Molecular Structure Theory that demonstrating its superiority in accounting for each of these three aspects of smell. (shrink)

Biologists and historians often present natural history and molecular biology as distinct, perhaps conflicting, fields in biological research. Such accounts, although supported by abundant evidence, overlook important areas of overlap between these areas. Focusing upon examples drawn particularly from systematics and molecular evolution, I argue that naturalists and molecular biologists often share questions, methods, and forms of explanation. Acknowledging these interdisciplinary efforts provides a more balanced account of the development of biology during the post-World War II era.

In this fascinating study, the author analyzes the conceptual roots of molecular biology and the social matrix in which it was developed.

Este artigo tem como objetivo fazer uma reflexão sobre uma metodologia para analisar a relação entre pós-modernidade e comunicação. Com isso, busca fortalecer um método que pode auxiliar na compreensão da organização da sociedade pós-moderna, relacionada ao uso de dois meios de comunicação. Para atender a esses objetivos, pretendemos partir das visões de Marshall Mcluhan, estudamos dois meios de comunicação; Michael Foucault, sua Arqueologia do Saber constitui dois paradigmas de uma época; e por Giorgio Agamben e seu método baseado na (...) relação entre paradigma, arqueologia e matéria. Este debate torna-se relevante para que seja possível desenvolver um método científico das Ciências da Comunicação que questione o contexto contemporâneo de dois saberes académicos. (shrink)

Perhaps the hottest topic in the philosophy of chemistry is that of the relationship between chemistry and physics. The problem finds one of its main manifestations in the debate about the nature of molecular structure, given by the spatial arrangement of the nuclei in a molecule. The traditional strategy to address the problem is to consider chemical cases that challenge the definition of molecular structure in quantum–mechanical terms. Instead of taking that top-down strategy, in this paper we face the problem (...) of the reduction of molecular structure to quantum mechanics from a bottom-up perspective: our aim is to show how the theoretical peculiarities of quantum mechanics stand against the possibility of molecular structure, defined in terms of the spatial relations of the nuclei conceived as individual localized objects. We will argue that, according to the theory, quantum “particles” are not individuals that can be identified as different from others and that can be reidentified through time; therefore, they do not have the ontological stability necessary to maintain the relations that can lead to a spatially definite system with an identifiable shape. On the other hand, although quantum chemists use the resources supplied by quantum mechanics with successful results, this does no mean reduction: their “approximations” add certain assumptions that are not justified in the context of quantum mechanics or are even inconsistent with the very formal structure of the theory. (shrink)

Advances in molecular biology have generally been taken to support the claim that biology is reducible to chemistry. I argue against that claim by looking in detail at a number of central results from molecular biology and showing that none of them supports reduction because (1) their basic predicates have multiple realizations, (2) their chemical realization is context-sensitive and (3) their explanations often presuppose biological facts rather than eliminate them. I then consider the heuristic and confirmational implications of irreducibility and (...) argue that purely biochemical approaches are likely to be unsound and to be unable to confirm an important range of statements. I conclude by sketching criteria for scientific unity that do not entail reducibility and yet leave an important place for identifying underlying mechanisms. Molecular biology, properly understood, provides an excellent paradigm of non-reductive unity between different explanatory levels. (shrink)

Philosophical discussion of molecular and developmental biology began in the late 1960s with the use of genetics as a test case for models of theory reduction. With this exception, the theory of natural selection remained the main focus of philosophy of biology until the late 1970s. It was controversies in evolutionary theory over punctuated equilibrium and adaptationism that first led philosophers to examine the concept of developmental constraint. Developmental biology also gained in prominence in the 1980s as part of a (...) broader interest in the new sciences of self-organization and complexity. The current literature in the philosophy of molecular and developmental biology has grown out of these earlier discussions under the influence of twenty years of rapid and exciting growth of empirical knowledge. Philosophers have examined the concepts of genetic information and genetic program, competing definitions of the gene itself and competing accounts of the role of the gene as a developmental cause. The debate over the relationship between development and evolution has been enriched by theories and results from the new field of 'evolutionary developmental biology'. Future developments seem likely to include an exchange of ideas with the philosophy of psychology, where debates over the concept of innateness have created an interest in genetics and development. (shrink)

This paper focuses on the consolidation of Molecular Evolution, a field originating in the 1960s at the interface of molecular biology, biochemistry, evolutionary biology, biophysics and studies on the origin of life and exobiology. The claim is made that Molecular Evolution became a discipline by integrating different sorts of scientific traditions: experimental, theoretical and comparative. The author critically incorporates Timothy Lenoir’s treatment of disciplines , as well as ideas developed by Stephen Toulmin on the same subject. On their account disciplines (...) are spaces where the social and epistemic dimensions of science are deeply and complexly interwoven. However, a more detailed account of discipline formation and the dynamics of an emerging disciplinary field is lacking in their analysis. The present essay suggests focusing on the role of scientific concepts in the double configuration of disciplines: the social/political and the epistemic order. In the case of Molecular Evolution the concepts of molecular clock and informational molecules played a central role, both in differentiating molecular from classical evolutionists, and in promoting communication between the different sorts of traditions integrated in Molecular Evolution. The paper finishes with a reflection on the historicity of disciplines, and the historicity of our concepts of disciplines. (shrink)

This paper investigates what molecular biology has done for our understanding of the gene. I base a new account of the gene concept of classical genetics on the classical dogma that gene differences cause phenotypic differences. Although contemporary biologists often think of genes in terms of this concept, molecular biology provides a second way to understand genes. I clarify this second way by articulating a molecular gene concept. This concept unifies our understanding of the molecular basis of a wide variety (...) of phenomena, including the phenomena that classical genetics explains in terms of gene differences causing phenotypic differences. (shrink)

This essay considers how scholarly approaches to the development of molecular biology have too often narrowed the historical aperture to genes, overlooking the ways in which other objects and processes contributed to the molecularization of life. From structural and dynamic studies of biomolecules to cellular membranes and organelles to metabolism and nutrition, new work by historians, philosophers, and STS scholars of the life sciences has revitalized older issues, such as the relationship of life to matter, or of physicochemical inquiries to (...) biology. This scholarship points to a novel molecular vista that opens up a pluralist view of molecularizations in the twentieth century and considers their relevance to current science. (shrink)

Molecular Revolution in BrazilFélix Guattari and Suely Rolniktranslated by KarelClapshow and Brian HolmesYes, I believe that there is a multiple people, a people of mutants, apeople of potentialities that appears and disappears, that is embodied in social, literary, andmusical events.... I think that we're in a period of productivity, proliferation, creation, utterlyfabulous revolutions from the viewpoint of this emergence of a people. That's molecular revolution:it isn't a slogan or a program, it's something that I feel, that I live....--from MolecularRevolution in (...) BrazilFollowing Brazil's first democratic election after two decades of militarydictatorship, French philosopher Félix Guattari traveled through Brazil in 1982 with Brazilianpsychoanalyst Suely Rolnik and discovered an exciting, new political vitality. In the infancy of itsnew republic, Brazil was moving against traditional hierarchies of control and totalitarian regimesand founding a revolution of ideas and politics. Molecular Revolution in Brazil documents theconversations, discussions, and debates that arose during the trip, including a dialogue betweenGuattari and Brazil's future President Luis Ignacia Lula da Silva, then a young gubernatorialcandidate. Through these exchanges, Guattari cuts through to the shadowy practices of globalizationgone awry and boldly charts a revolution in practice.Assembled and edited by Rolnik, MolecularRevolution in Brazil is organized thematically; aphoristic at times, it presents a lesser-known,more overtly political aspect of Guattari's work. Originally published in Brazil in 1986 asMicropolitica: Cartografias do desejo, the book became a crucial reference for political movementsin Brazil in the 1980s and 1990s. It now provides English-speaking readers with an invaluablepicture of the radical thought and optimism that lies at the root of Lula's Brazil. Félix Guattari, post-'68 French psychoanalyst and philosopher, is the author of Anti-Oedipus, The Anti-Oedipus Papers, 2006), and other books. Semiotext haspublished the first two volumes of his complete essays, Chaosophy and Soft Subversions, and will publish the final volume, Chaos and Complexity, in 2008. Suely Rolnik is apsychoanalyst, cultural critic, and curator who lives and works in São Paulo, Brazil. She was aclose collaborator of Guattari during her exile in Paris from the military dictatorship inBrazil. (shrink)

The paper argues against the central dogma and its interpretation by C. Kenneth Waters and Alex Rosenberg. I argue that certain phenomena in the regulation of gene expression provide a break with the central dogma, according to which sequence specificity for a gene product must be template derived. My thesis of 'molecular epigenesis' with its three classes of phenomena, sequence 'activation', 'selection', and 'creation', is exemplified by processes such as transcriptional activation, alternative cis- and trans-splicing, and RNA editing. It argues (...) that other molecular resources share the causal role of genes; the sequence specificity for the linear sequence of any gene product is distributed between the coding sequence, cis-acting sequences, trans-acting factors, environmental signals, and the contingent history of the cell (thesis of distributed causal specificity). I conclude that the central dogma has unnecessarily restricted genetic research to the sequencing of protein-coding genes, unilinear pathway analyses, and the focus on exclusive specificity. (shrink)

The first part of this paper has shown that the development of regulatory genetics and the lactose operon model stemmed from laboratory cultures rooted in local traditions. A "physiological" culture may be recognized in the Pasteurian context. The institutional continuity provided the basis for a tenuous link between Pasteur, Lwoff, and Monod. My claim is that the "national" value of regulatory and physiological genetics is an artifact produced in the course of the legitimization process accompanying the institutionalisation of the discipline. (...) In the 1960s, the lactose operon model was turned into a "flag-object," a symbol of the new culture. The work done by the Pasteurian group became therefore the most important, if not the only, exemplar of molecular biology in France.The second part o f the paper described the origins of general patterns that dominated the building of molecular biology in France. The study of the relationships between molecular biologists and biochemists or immunologists revealed the existence of alternatives to the development of operon research, or to the convergence with molecular biology. Both examples uncover specific paths leading to achievements that might be viewed as international trends: the expansion of RNA and translation studies, and the development of cellular immunology. They illustrate two possible patterns of linking local settings and disciplinary traditions: an oligopolistic situation where a few groups or one institution dominate an entire field, and the emergence of "collective" trends through collaboration networks or schools. (shrink)

Since the publication of Nikolas Rose’s ‘The Politics of Life Itself’ there has been vivid discussion about how biopolitical governance has changed over the last decades. This article uses what Rose terms ‘molecular politics’, a new socio-technical grip on the human body, as a contrasting background to ask anew his question ‘What, then, of biopolitics today?’ – albeit focusing not on advances in genetics, microbiology, and pharmaceutics, as he does, but on the rapid proliferation of wearables and other sensor-software gadgets. (...) In both cases, new technologies providing information about the individual body are the common ground for governance and optimization, yet for the latter, the target is habits of moving, eating and drinking, sleeping, working and relaxing. The resulting profound differences are carved out along four lines: ‘somatic identities’ and a modified understanding of the body; the role of ‘expert knowledge’ compared to that of networks of peers and self-experimentation; the ‘types of intervention’ by which new technologies become effective in our everyday life; and the ‘post-discipline character’ of molecular biopolitics. It is argued that, taken together, these differences indicate a remarkable shift which could be termed aretaic: its focus is not ‘life itself’ but ‘life as it is lived’, and its modality are new everyday socio-technical entanglements and their more-than-human rationalities of governance. (shrink)

Recent work on gene concepts has been influenced by recognition of the extent to which RNA transcripts from a given DNA sequence yield different products in different cellular environments. These transcripts are altered in many ways and yield many products based, somehow, on the sequence of nucleotides in the DNA. I focus on alternative splicing of RNA transcripts (which often yields distinct proteins from the same raw transcript) and on 'gene sharing', in which a single gene produces distinct proteins with (...) the exact same amino acid sequence. These are instances of molecular pleiotropy, in which distinct molecules are derived from a single putative gene. In such cases the cellular and external environments play major roles in determining which protein is produced. Where there is molecular pleiotropy, alternative gene concepts are naturally deployed; molecular epigenesis (revision of sequence-based information by altering molecular conformations or by action of non-informational molecules) plays a major role in orderly development. These results show that gene concepts in molecular biology do, and should, have both structural and functional components. They also show the need for a plurality of gene concepts and reveal fundamental difficulties in stabilizing gene concepts solely by reference to nucleotide sequence. (shrink)

Without directly addressing the Demarcation Problem for logic—the problem of distinguishing logical vocabulary from others—we focus on distinctive aspects of logical vocabulary in pursuit of a second goal in the philosophy of logic, namely, proposing criteria for the justification of logical rules. Our preferred approach has three components. Two of these are effectively Belnap’s, but with a twist. We agree with Belnap’s response to Prior’s challenge to inferentialist characterisations of the meanings of logical constants. Belnap argued that for a logical (...) constant to exist, its rules must be conservative over a previously given consequence relation and guarantee the uniqueness of the constant. The twist is that we require logical vocabulary to be provably conservative, not over a previously given formal consequence relation, but over a previously given meaningful vocabulary of a language. Uniqueness is also a feature defined in terms of provability: if two syntactically distinguished expressions are governed by the same rules, then formulas with them as main operators are interderivable. Belnap’s criteria are not only those for the existence of a logical constant, but more: they are what distinguishes logical vocabulary from all other expressions. It is the defining mark of a logical constant that it is provably conservative over the fragment of the language which excludes it and that its rules guarantee its uniqueness. The third component is the topic neutrality of logic. The provable conservativeness of logic over a previously given vocabulary of a language is motivated, in part, by appeal to molecularism in the theory of meaning. Molecularity is a feature endorsed by the theory of meaning as a whole, so it does not distinguish logical constants from other expressions. The same is true for conservativeness. We argue that molecularity, and hence conservativeness, are implicit presuppositions of speakers’ use of language: the addition of new vocabulary to a language is presupposed to be conservative. But this presupposition is one that we should be able reflectively to endorse (such as when attempting a rational reconstruction of the use of the vocabulary). Thus, where conservativeness is found to fail, this defect should be remedied and the use of the vocabulary corrected (as in classical negation) or excised altogether (as in pejoratives). We go on to characterise a notion of topic neutrality, which we argue applies to logical vocabulary. We then note that reflective endorsement of the conservativeness of a topic neutral vocabulary requires a proof that the vocabulary is conservative relative to any base vocabulary. Thus we require that logical vocabulary be demonstrably conservative. Allying this requirement, distinctive of logic, to a general consideration about the commitments of assertion yields a mode of justification for logical constants akin to some conceptions of Harmony, i.e., to the idea that the consequences of assertion of a logical complex need to be warranted by the grounds and ought to be the strongest consequences warranted by the grounds. Intuitionistic logic acquires a somewhat familiar justification but emanating from a new motivation. (shrink)

Senior molecular geneticists were interviewed about their perceptions of the ethical and social implications of genetic knowledge. Inductive analysis of these interviews identified a number of strategies through which the scientists negotiated their moral responsibilities as they participated in generating knowledge that presents difficult ethical questions. These strategies included: further analysis and application of scientific method; clarification of multiple roles; negotiation with the public through public debate, institutional processes of funding, ethics committees and legislation; and personal responsibility.

The practice and development of modern medicine requires large amounts of data, particularly in the domain of cancer. The future of personalized medicine lies neither with “genomic medicine” nor with “precision medicine”, but with “data medicine”. The establishment of this DM has required far-reaching changes, to establish four essential elements connecting patients and doctors: biobanks, databases, bioinformatic platforms and genomic platforms. The “transformation” of scientific research areas, such as genetics, bioinformatics and biostatistics, into clinical specialties has generated a new vision (...) of care. Molecular tumor boards are one response to these changes and are now providing better access to next-generation sequencing and new cancer treatments to patients with inoperable or metastatic cancers, and those for whom the usual treatment has failed. However, MTB face a crucial ethical challenge: maintaining and improving the trust of patients, clinicians, researchers and industry in academic medical centers supported by private or public funding rather than providing genetic data directly to private companies. We believe that, in this era of DM, appropriate modern digital communication networks will be required to maintain this trust and to improve the organization and effectiveness of the system. There is, therefore, a need to reconsider the form and content of informed consent documents at all academic medical centers and to introduce dynamic and electronic informed consent. (shrink)

Marx não apenas flertou com o modo de expressão Hegeliano na sua obra O Capital, mas ele próprio pretendia trabalhar o racional da lógica dialéctica de Hegel. O artigo tenta esboçar a inversão de Marx do programa teórico de Hegel mostrando, primeiro, que esta inversão não deve ser entendida num sentido metafísico como programa de um materialismo dialéctico e histórico, como fizeram primeiro Engels e depois o marxismo tradicional. Em segundo lugar, será demonstrado que a inversão de Marx do programa (...) teórico de Hegel toma mais emprestado a este último do que é normalmente assumido, em particular Marx partilha a crítica de Hegel à concepção instrumental do conhecer que está subjacente ao cepticismo metodológico em relação ao conhecer na filosofia e ciência moderna e contemporânea. O artigo defende uma renovação do marxismo com base num Hegel-marxismo. (shrink)

By their own account, physicalists are committed to the claim that physics is causally complete, or closed. The claim is presented as an empirical one. However, detailed and explicit empirical arguments for the claim are rare. I argue that molecular models are a key source of evidence but that, on closer inspection, they do not support the completeness claim.

Much of the recent philosophical debate on causation and causal explanation in the biological and biomedical sciences has focused on the notion of mechanism. Mechanisms, their nature and epistemic roles have been tackled by a range of so-called neo-mechanistic theories, and widely discussed. Without denying the merits of this approach, our paper aims to show how lately it has failed to give proper credit to processes, which are central to the field, especially of contemporary molecular biology. Processes can be summed (...) up in the notion of ‘pathway’, which is far from being just equivalent to that of ‘mechanism’ and has a profound epistemological and explanatory relevance. It is argued that an adequate consideration of pathways impels some rethinking of scientific explanation in molecular biology, namely its functional and contextual features. A number of examples are given to suggest that the focus of philosophical attention in this disciplinary field should shift from the notion of mechanism to the notion of pathway. (shrink)

Whether or not quantum physics can account for molecular structure is a matter of considerable controversy. Three of the problems raised in this regard are the problems of molecular structure. We argue that these problems are just special cases of the measurement problem of quantum mechanics: insofar as the measurement problem is solved, the problems of molecular structure are resolved as well. In addition, we explore one consequence of our argument: that claims about the reduction or emergence of molecular structure (...) cannot be settled independently of the choice of a particular resolution to the measurement problem. Specifically, we consider how three standard putative solutions to the measurement problem inform our under- standing of a molecule in isolation, as well as of chemistry’s relation to quantum physics. (shrink)

We apply molecular code theory to a rule-based model of the human inner kinetochore and study how complex formation in general can give rise to molecular codes. We analyze 105 reaction networks generated from the rule-based inner kinetochore model in two variants: with and without dissociation of complexes. Interestingly, we found codes only when some but not all complexes are allowed to dissociate. We show that this is due to the fact that in the kinetochore model proteins can only bind (...) at kinetochores by attaching to already attached proteins and cannot form complexes in free solution. Using a generalized linear mixed model we study which centromere protein can take which role in a molecular code . By this, associations between CENPs and code roles are found. We observed that CenpA is a major risk factor while CenpQ is a major protection factor . Finally we show, using an abstract model of copolymer formation, that molecular codes can also be realized solely by the formation of stable complexes, which do not dissociate. For example, with particular dimers as context a molecular code mapping from two different monomers to two particular trimers can be realized just by non-selective complex formation. We conclude that the formation of protein complexes can be utilized by the cell to implement molecular codes. Living cells thus facilitate a subsystem allowing for an enormous flexibility in the realization of mappings, which can be used for specific regulatory processes, e.g. via the context of a mapping. (shrink)

The molecular genetic age can be said to have begun with the letter in Nature in 1953 by Watson and Crick, describing the helical structure of DNA. Some outstanding scientific work preceded that discovery, including especially the recognition by Chargaff of base-pair complementarity, but no discovery quite captured the imagination of the biomedical world as a few understated words by Watson and Crick in their famous one-page paper: "It has not escaped our notice that the specific pairing we have postulated (...) immediately suggests a possible copying mechanism for the genetic material". The manner in which genetic material was passed on from generation to generation had been decoded.That discovery was... (shrink)

Biologists employ a suggestive metaphor to describe the complexities of molecular interactions within cells and embryos: cytological components are said to be part of “ecosystems” that integrate them in a complex network of relations with many other entities. The aim of this essay is to scrutinize the molecular ecosystem, a metaphor that, despite its longstanding history, has seldom be articulated in detail. I begin by analyzing some relevant analogies between the cellular environment and the biosphere. Next, I discuss the applicability (...) of the molecular ecosystem concept in actual scientific practice. (shrink)

Significant progress in the molecular investigation of endogenous bioelectric signals during pattern formation in growing tissues has been enabled by recently developed techniques. Ion flows and voltage gradients produced by ion channels and pumps are key regulators of cell proliferation, migration, and differentiation. Now, instructive roles for bioelectrical gradients in embryogenesis, regeneration, and neoplasm are being revealed through the use of fluorescent voltage reporters and functional experiments using well‐characterized channel mutants. Transmembrane voltage gradients (Vmem) determine anatomical polarity and function as (...) master regulators during appendage regeneration and embryonic left‐right patterning. A state‐of‐the‐art recent study reveals that they can also serve as prepatterns for gene expression domains during craniofacial patterning. Continued development of novel tools and better ways to think about physical controls of cell‐cell interactions will lead to mastery of the morphogenetic information stored in physiological networks. This will enable fundamental advances in basic understanding of growth and form, as well as transformative biomedical applications in regenerative medicine. (shrink)

The Neo‐Darwinian concept of natural selection is plausible when one assumes a straightforward causation of phenotype by genotype. However, such simple 1:1 mapping must now give place to the modern concepts of gene regulatory networks and gene expression noise. Both can, in the absence of genetic mutations, jointly generate a diversity of inheritable randomly occupied phenotypic states that could also serve as a substrate for natural selection. This form of epigenetic dynamics challenges Neo‐Darwinism. It needs to incorporate the non‐linear, stochastic (...) dynamics of gene networks. A first step is to consider the mathematical correspondence between gene regulatory networks and Waddington's metaphoric ‘epigenetic landscape’, which actually represents the quasi‐potential function of global network dynamics. It explains the coexistence of multiple stable phenotypes within one genotype. The landscape's topography with its attractors is shaped by evolution through mutational re‐wiring of regulatory interactions – offering a link between genetic mutation and sudden, broad evolutionary changes. (shrink)

This paper consists in the Spanish translation of a manuscript by Franz Brentano, where he deals with “The Method of Study of Aristotle and, More Generally, the Method of Historical Research in Philosophical Field”. In these pages, Brentano challenges the Aristotelian studies of his time by criticizing the approach followed by E. Zeller and other scholars. Meanwhile, he suggests some hermeneutical rules in order to interpret Aristotle in the right way. The core of his proposal is the use of philosophical (...) hermeneutics, that is, the interpreter should philosophize following the Aristotelian arguments, like the Peripatetics used to do. In his introduction to the text by Brentano, the Spanish translator also recommends a new chronology for the manuscript, i.e. not much later than 1883. Complete title: «Franz Brentano: Sobre el método en los estudios aristotélicos y sobre el método de la investigación histórica en ámbito filosófico en general». Original title: Franz Brentano, «Zur Methode aristotelischen Studien, und zur Methode geschichtlicher Forschung auf philosophischem Gebiet überhaupt», in: 'Über Aristoteles. Nachgelassene Aufsätze', edited by Rolf George, Hamburg: Meiner, 1986, pp. 7-20. (shrink)

Although molecular systematists may use the terminology of cladism, claiming that the reconstruction of phylogenetic relationships is based on shared derived states , the latter is not the case. Rather, molecular systematics is based on the assumption, first clearly articulated by Zuckerkandl and Pauling , that degree of overall similarity reflects degree of relatedness. This assumption derives from interpreting molecular similarity between taxa in the context of a Darwinian model of continual and gradual change. Review of the history of molecular (...) systematics and its claims in the context of molecular biology reveals that there is no basis for the “molecular assumption.”. (shrink)

The intellectual origins of molecular biology are usually traced back to the 1930s. By contrast, molecular biology acquired a social reality only around 1960. To understand how it came to designate a community of researchers and a professional identity, I examine the creation of the first institutes of molecular biology, which took place around 1960, in four European countries: Germany, the United Kingdom, France, and Switzerland. This paper shows how the creation of these institutes was linked to the results of (...) post-war economic reconstruction. Then, it compares how the promoters of these different institutional projects delimited the goals of their discipline, reflected on its history, and suggested how research should be organised. I show how they carefully positioned their new discipline within the emerging national science policy discourse of the 1950s, and aligned it with the current vision of scientific modernity. In particular, I discuss how they articulated the meaning of molecular biology with respect to five common themes: the role of physics in the atomic age, the relations between fundamental research and medical applications, the ‘Americanisation’ of scientific research, the value of science in the reconstruction of national identities, and the drive towards interdisciplinary research. This paper thus demonstrates that beyond the local and national accounts there is a European history of molecular biology. (shrink)

Paleontological and molecular data suggest quite different patterns for the early evolution of placental mammals. Paleontological evidence indicates a radiation, with most of the extant orders diverging at approximately the same time, close to the Cretaceous-Tertiary boundary, 65 Myr ago. Molecular evidence suggests a branching pattern of evolution that started much earlier. Resolving this discrepancy requires a consideration of the assumptions that underlie both approaches. It is argued here that the pattern indicated by the molecular approach is the most likely (...) to be correct. If it is correct then either: 1) A diversity of placental mammals remains to be sampled from the Cretaceous, or 2) The placental orders diverged phylogenetically long before they diversified morphologically, implying a decoupling of the evolutionary processes associated with speciation and adaptation. The adaptive diversification of placental mammals may have required the demise of the dinosaurs at the end of the Cretaceous, but it occurred in lineages that had a long prior history of independent existence. BioEssays 21: 1052–1058, 1999. © 1999 John Wiley & Sons, Inc. (shrink)

En este artículo analizamos la crítica que Richard Rorty hace de la apelación al “método experimental” por parte de John Dewey. Defendemos que la categórica desestimación que Rorty presenta del vínculo entre el pragmatismo de Dewey y su concepción de método hubiera sido o bien matizada, o bien radicalmente diferente, de haber considerado seriamente la importancia que la reflexión sobre la educación tenía para el filósofo de Vermont. Nuestra estrategia interpretativa se apoya en la recuperación que Henry Cowles hace recientemente (...) de la apelación al método experimental que Dewey lleva a cabo en How We Think —uno de sus textos educativos más importantes—, en donde se muestra las vinculaciones relevantes entre pragmatismo, evolucionismo y método. Este marco histórico-conceptual nos permitirá cuestionar la reconstrucción de Rorty en torno de este aspecto de la filosofía deweyana tomando en cuenta, fundamentalmente, sus propias reflexiones sobre educación. (shrink)

This paper extends previous arguments against the assumption that the study of variation at the molecular level was instigated with a view to solving an internal conflict between the balance and classical schools of population genetics. It does so by focusing on the intersection of basic research in protein chemistry and the molecular approach to disease with the enactment of global health campaigns during the Cold War period. The paper connects advances in research on protein structure and function as reflected (...) in Christian Anfinsen’s The molecular basis of evolution, with a political reading of Emilé Zuckerkandl and Linus Pauling’s identification of molecular disease and evolution. Beyond atomic fallout, these advances constituted a rationale for the promotion of genetic surveys of human populations in the Third World, in connection with international health programs. Light is shed not only on the experimental roots of the molecular challenge but on the broader geopolitical context where the rising role of biomedicine and public health had an impact on evolutionary biology. (shrink)

In this article, two issues regarding mechanisms are discussed. The first concerns the relationships between “mechanism description” and “mechanism explanation.” It is proposed that it is rather plausible to think of them as two distinct epistemic acts. The second deals with the different molecular biology explanatory contexts, and it is shown that some of them require physics and its laws.

El surgimiento de la biología molecular en la frontera que separa la teoría genética y la bioquímica constituye un buen banco de pruebas para distintas estrategias metacientíficas. El teoreticismo de las revoluciones científicas de Thomas S. Kuhn propende hacia un constructivismo social que no sirve para dar cuenta de la posible verdad y corrección del teorema de la doble hélice. El enfoque semántico (desarrollado por J. Sneed, W. Stegmüller, U Moulines, etc.), aunque pretende adecuar sus análisis a los contenidos estructurales (...) y al significado de los teoremas científicos, acaba disolviendo estos en meras correspondencias formales. La teoría del cierre categorial, en cambio, se adscribe a un constructivismo circularista que permite entender los dogmas sobre la estructura del ADN como si fueran identidades sintéticas materiales sin desdeñar por ello los aspectos pragmáticos, históricos y sociales, que valoran en su justa medida las aportaciones del grupo Fago, de Watson y Crick, de Pauling o de las universidades implicadas. (shrink)

Fanconi anaemia (FA) comprises a group of autosomal recessive disorders resulting from mutations in one of eight genes (FANCA, FANCB, FANCC, FANCD1, FANCD2, FANCE, FANCF and FANCG). Although caused by relatively simple mutations, the disease shows a complex phenotype, with a variety of features including developmental abnormalities and ultimately severe anaemia and/or leukemia leading to death in the mid teens. Since 1992 all but two of the genes have been identified, and molecular analysis of their products has revealed a complex (...) mode of action. Many of the proteins form a nuclear multisubunit complex that appears to be involved in the repair of double‐strand DNA breaks. Additionally, at least one of the proteins, FANCC, influences apoptotic pathways in response to oxidative damage. Further analysis of the FANC proteins will provide vital information on normal cell responses to damage and allow therapeutic strategies to be developed that will hopefully supplant bone marrow transplantation. BioEssays 24:439–448, 2002. © 2002 Wiley Periodicals, Inc. (shrink)

The SARS‐CoV‐2 virus is responsible for the COVID‐19 pandemic the world experience since 2019. The protein responsible for the first steps of cell invasion, the spike protein, has probably received the most attention in light of its central role during infection. Computational approaches are among the tools employed by the scientific community in the enormous effort to study this new affliction. One of these methods, namely molecular dynamics (MD), has been used to characterize the function of the spike protein at (...) the atomic level and unveil its structural features from a dynamic perspective. In this review, we focus on these main findings, including spike protein flexibility, rare S protein conformational changes, cryptic epitopes, the role of glycans, drug repurposing, and the effect of spike protein variants. (shrink)