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.

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)

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)

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.

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)

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)

This article looks at Deleuze and Guattari's understanding of molecular biology, focusing particularly on their reading of two highly influential works by the eminent French molecular biologists François Jacob and Jacques Monod, La logique du vivant and Le hasard et la nécessité. In these two works, Jacob and Monod present the significance of molecular biology in broadly reductionist terms. What is more, the lac operon model of gene regulation that they propose serves to reinforce the so-called Central (...) Dogma of molecular biology, according to which information passes from DNA to RNA to proteins, with no reverse route. However, Deleuze and Guattari discover intensive potentials within the descriptions of molecular biology offered by both writers. It is argued that Jacob's work in particular, as it has developed in the years since the publication of La logique du vivant in 1970, has itself developed these intensive potentials. (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)

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)

I offer a defense, albeit a qualified one, of machine analogies in biology, focusing on molecular contexts. The defense is rooted in my prior work (Levy in Philosopher’s Imprint 14(6), 2014), which construes the machine machine-likeness of a system as a matter of the extent to which it exhibits an internal division of labor. A concrete aim is to shore up the notion of molecular biological machines, paying special attention to processive molecular motors, such as Kinesin. But (...) I will also try to show how the division of labor account gives us guidance more broadly, both about where and why machine analogies can be expected to prove helpful and about their limitations. (shrink)

Since the publication of Nikolas Rose’s ‘The Politics of Life Itself’ (2001) 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 (self-)governance. (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)

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.

Since molecules are inaccessible to immediate observation, our conception of the molecule is brought about by transdiction which entails invention of various transcendental ideas. In organic chemistry we think that molecules consist of atoms, bonds, functional groups, etc. This is, however, not the unique description of the molecule as is shown by quantum mechanical calculations, for example. Then, what description represents the real molecule? Before asking this question, we have to consider what the real molecule is in the first place. (...) Constructive realism distinguishes our cognitive world and the world just given, and claims that we should accept the former as reality. Understanding our cognitive world is possible only through construction of micro-worlds. Atoms, bonds, functional groups, etc., are micro-worlds which make sense in a theoretical framework of organic chemistry. In this study we translate a micro-world to an affordance and paraphrase it as a context-relative dispositional attribute of an {agent-world} complex. Then, we can understand that it is what we take as molecular structure, not what might be out there to be found, that we should accept as reality. Excluding metaphysical fictions from scientific arguments, constructive realism makes science a meaningful activity. Constructive realism claims that, for getting knowledge of the world, we have to integrate information into our own linguistic frame, i.e., to translate it. Strangification is a technique of intentionally taking an accepted proposition out of one scientific system and putting it into a completely different context. As is the case with translation, strangification brings about deeper understanding of philosophical as well as scientific grounds on which the proposition system holds. We apply this method to molecular structure and reveal that it is an ingenious model to describe molecular behavior in multi-molecular systems with strong interactions between molecules. Information provided by strangification is essential to claim the legitimacy of a proposition system. As far as strangification is properly applied, relativism is irrelevant to constructive realism. (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)

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)

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)

This chapter contains section titled: The Neutral Theory of Molecular Evolution The Molecular Clock The Neutral Null Model Controversy in Molecular Evolution Acknowledgment References Further Reading.

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)

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)

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)

The practice of theoretical research in chemistry largely consists in the construction of models without which experimentation would be impossible. The best-known theoretical models in chemistry are those of the molecular structures of chemical compounds. What is the correspondence between these models and the unobservable entities that they are meant to explain? What is the ontological status of molecular models? The anti-realists question the basis of the realists’ belief in these entities and the truth claims regarding them. Ultimately, (...) the realist/anti-realist debate points to the question of the scope of scientific knowledge. In this paper, I shall show that the description of natural entities offered by the contemporary scientific worldview reveals that molecular modeling presupposes a realistic epistemology that recognizes the limits of scientific objectification. (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)

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.

The concept of molecular structure is one of the most important concepts of chemistry. In fact, molecular structure is closely related to the concept of chemical substance and its set of properties, and it is the main factor in the explanation of reactivity. In fact, much of the behavior of substances is explained in terms of the structure of their component molecules. This may explain why people tend to take the notion of molecular structure for granted. However, (...) the problem begins already when it comes to specifying the concept, since there is no clear definition of ‘molecular structure’ valid for all chemistry. The purpose of the present article is to show that the term ‘molecular structure’ subsumes very different notions, which depend on how the molecule and its components are conceived, and each of which brings its own difficulties. In particular, we will focus on how the molecule and its structure are devised from a classical view and from a quantum–mechanical view, and will discuss the different problems related with molecular structure that arise in each case. (shrink)

We provide an introduction to network theory, evidence to support a connection between molecular network structure and neuropsychiatric disease, and examples of how network approaches can expand our knowledge of the molecular bases of these diseases. Without systematic methods to derive their biological meanings and inter‐relatedness, the many molecular changes associated with neuropsychiatric disease, including genetic variants, gene expression changes, and protein differences, present an impenetrably complex set of findings. Network approaches can potentially help integrate and reconcile (...) these findings, as well as provide new insights into the molecular architecture of neuropsychiatric diseases. Network approaches to neuropsychiatric disease are still in their infancy, and we discuss what might be done to improve their prospects. (shrink)

Despite its prominence in scientific research, molecular medicine has not received sufficient attention by the philosophical community. _Philosophy of Molecular Medicine: Foundational Issues in Theory and Practice_ aims at a systematic investigation of a number of foundational issues in the field of molecular medicine. The volume is organized around four broad modules focusing, respectively, on the following key aspects: What are the nature, scope and limits of molecular medicine? How does it provide explanations? How does it (...) represent and model phenomena of interest? How does it infer new knowledge from data and experiments? The essays collected here, authored by prominent scientists and philosophers of science, focus on a handful of mainstream topics in the philosophical literature, such as _causation_, _explanation_, _modeling_, and _scientific inference_. These previously unpublished contributions shed new light on these traditional topics by integrating them with problems, methods, and results from three prominent areas of contemporary biomedical science: _basic research_, _translational_ and _clinical research_, and _clinical practice_. (shrink)

Molecular approaches have revolutionised evolutionary biology since the late 50s. Today, molecular evolutionary biology is an integrated hybrid of mechanistic, mathematical and datafied research. I aim to show that the molecular conceptualisation of evolutionary dynamics provided by this hybrid has a significant mechanistic foundation. I shall first outline the biochemical roots of this foundation. Then, I shall illustrate how evolutionary causal chains are conceptualised in contemporary molecular evolution research. I shall finally argue that a fundamental innovation (...) of molecular evolutionary models is dependent on the mechanistic understanding of the mutational and developmental processes causing the origin of traits. Thus, molecular evolutionary biology integrates proximate and ultimate causes, providing a variety of how-possibly and how-actually explanations. (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)

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)

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)

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)

Protistology, and evolutionary protistology in particular, is experiencing a golden research era. It is an extended one that can be dated back to the 1970s, which is when the molecular rebirth of microbial phylogeny began in earnest. John Archibald, a professor of evolutionary microbiology at Dalhousie University (Nova Scotia, Canada), focuses on the beautiful story of endosymbiosis in his book, John Archibald, One Plus One Equals One: Symbiosis and the Origin of Complex Life (Oxford: Oxford University Press, 2014). However, (...) this historical narrative could be treated as synecdochal of how the molecular revolution has changed evolutionary biology forever, and that is how Archibald has structured his book. I will address the encompassing theme of molecular methods in detail, but also pay careful attention to the endosymbiosis thread in its own right. (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)

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)

One of the most plausible and widely discussed examples of strong emergence is molecular structure. The only detailed account of it, which has been very influential, is due to Robin Hendry and is formulated in terms of downward causation. This paper explains Hendry’s account of the strong emergence of molecular structure and argues that it is coherent only if one assumes a diachronic reflexive notion of downward causation. However, in the context of this notion of downward causation, the (...) strong emergence of molecular structure faces three challenges that have not been met and which have so far remained unnoticed. First, the putative empirical evidence presented for the strong emergence of molecular structure equally undermines supervenience, which is one of the main tenets of strong emergence. Secondly, it is ambiguous how the assumption of determinate nuclear positions is invoked for the support of strong emergence, as the role of this assumption in Hendry’s argument can be interpreted in more than one way. Lastly, there are understandings of causation which render the postulation of a downward causal relation between a molecule’s structure and its quantum mechanical entities, untenable. (shrink)

A recent literature review of commentaries and ‘state of the art’ articles from researchers in psychiatric genetics (PMG) offers a consensus about progress in the science of genetics, disappointments in the discovery of new and effective treatments, and a general optimism about the future of the field. I argue that optimism for the field of psychiatric molecular genetics (PMG) is overwrought, and consider progress in the field in reference to a sample estimate of US National Institute of Mental Health (...) funding for this paradigm for the years 2008 and 2009. I conclude that the amounts of financial investment in PMG is questionable from an ethical perspective, given other research and clinical needs in the USA. (shrink)

The term molecular genetics sometimes refers to (1) a fundamental theory alleging that genes direct all life processes through the production of proteins and RNAs (ribonucleic acids), sometimes to (2) a more modest, basic theory about the replication and expression of DNA (deoxyribonucleic acid), and sometimes to (3) an investigative approach applied throughout biomedical science that is based on investigative strategies grounded in the basic theory about genes. This entry briefly summarizes the basic knowledge of molecular genetics and (...) surveys philosophical research on the subject, considering all three senses of the term. The focus is on the traditional issue of theoretical reduction as an account of the molecularization of genetics as well as on more recent work that attends to investigative rather than theoretical and explanatory reasoning. (shrink)

It is proposed that the controlling system of the nerve cell is a molecular quantum device with an inner point of view. For the description of such a system it is necessary to create new science.

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)

Between 1905 and 1913, French physicist Jean Perrin's experiments on Brownian motion ostensibly put a definitive end to the long debate regarding the real existence of molecules, proving the atomic theory of matter. While Perrin's results had a significant impact at the time, later examination of his experiments questioned whether he really gained experimental access to the molecular realm. The experiments were successful in determining the mean kinetic energy of the granules of Brownian motion; however, the values for (...) class='Hi'>molecular magnitudes Perrin inferred from them simply presupposed that the granule mean kinetic energy was the same as the mean molecular kinetic energy in the fluid in which the granules move. This stipulation became increasingly questionable in the years between 1908 and 1913, as significantly lower values for these magnitudes were obtained from other experimental results like alpha-particle emissions, ionization, and Planck's blackbody radiation equation. In this case study in the history and philosophy of science, George E. Smith and Raghav Seth here argue that despite doubts, Perrin's measurements were nevertheless exemplars of theory-mediated measurement-the practice of obtaining values for an inaccessible quantity by inferring them from an accessible proxy via theoretical relationships between them. They argue that it was actually Perrin more than any of his contemporaries who championed this approach during the years in question. The practice of theory-mediated measurement in physics had a long history before 1900, but the concerted efforts of Perrin, Rutherford, Millikan, Planck, and their colleagues led to the central role this form of evidence has had in microphysical research ever since. Seth and Smith's study thus replaces an untenable legend with an account that is not only tenable, but more instructive about what the evidence did and did not show. (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)

Problems of consciousness are broadly classified into two: easy and hard. The subjective nature of experience is considered the hard problem of consciousness. Although several theories of consciousness have been proposed, none seem to satisfactorily answer the hard problem. To address this, here I explore the molecular process underlying experience and the biological purpose it serves the entity. Based on the molecular and cellular mechanisms that constitute the cognitive process, I hypothesise that an entity has a subjective mental (...) experience of an objective physical reality in two steps. First, the entity collects information regarding the physical characteristics of the context, via sensory organs, to produce a sensory experience. Second, it processes the information to infer the non-physical characteristics of the context, producing an affective experience. This process enables us to systematically identify factors that directly contribute to the subjective nature of experience and explore the hard problem of consciousness. Exploring the likely impact that an objective experience may bring about enables us to understand the significance of its subjective nature. According to this theory, the subjective nature of experience is likely to be responsible for cognitive diversity, providing the entities with a better chance of survival. In addition to the process and purpose of experience, the molecular theory addresses other characteristics of experience. Such as its ability to occur in the absence of physical reality and explains why experience accompanies functions of consciousness. Based on the molecular process of experience, consciousness can be considered as a set of cognitive processes that administer the non-genetic set of information required for the conscious entity to survive. (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)