Online research in philosophy

After the discovery of the structure of DNA in 1953, scientists working in molecular biology embraced reductionism—the theory that all complex systems can be understood in terms of their components. Reductionism, however, has been widely resisted by both nonmolecular biologists and scientists working outside the field of biology. Many of these antireductionists, nevertheless, embrace the notion of physicalism—the idea that all biological processes are physical in nature. How, Alexander Rosenberg asks, can these self-proclaimed physicalists also be antireductionists? (...) With clarity and wit, Darwinian Reductionism navigates this difficult and seemingly intractable dualism with convincing analysis and timely evidence. In the spirit of the few distinguished biologists who accept reductionism—E. O. Wilson, Francis Crick, Jacques Monod, James Watson, and Richard Dawkins—Rosenberg provides a philosophically sophisticated defense of reductionism and applies it to molecular developmental biology and the theory of natural selection, ultimately proving that the physicalist must also be a reductionist. (shrink)

Understanding how scientific activities use naming stories to achieve disciplinary status is important not only for insight into the past, but for evaluating current claims that new disciplines are emerging. In order to gain a historical understanding of how new disciplines develop in relation to these baptismal narratives, we compare two recently formed disciplines, systems biology and genomics, with two earlier related life sciences, genetics and molecular biology. These four disciplines span the twentieth century, a period in (...) which the processes of disciplinary demarcation fundamentally changed from those characteristic of the nineteenth century. We outline how the establishment of each discipline relies upon an interplay of factors that include paradigmatic achievements, technological innovation, and social formations. Our focus, however, is the baptism stories that give the new discipline a founding narrative and articulate core problems, general approaches and constitutive methods. The highly plastic process of achieving disciplinary identity is further marked by the openness of disciplinary definition, tension between technological possibilities and the ways in which scientific issues are conceived and approached, synthesis of reductive and integrative strategies, and complex social interactions. The importance – albeit highly variable – of naming stories in these four cases indicates the scope for future studies that focus on failed disciplines or competing names. Further attention to disciplinary histories could, we suggest, give us richer insight into scientific development. (shrink)

Mechanistic models in molecular systems biology are generally mathematical models of the action of networks of biochemical reactions, involving metabolism, signal transduction, and/or gene expression. They can be either simulated numerically or analyzed analytically. Systems biology integrates quantitative molecular data acquisition with mathematical models to design new experiments, discriminate between alternative mechanisms and explain the molecular basis of cellular properties. At the heart of this approach are mechanistic models of molecular networks. We focus on (...) the articulation and development of mechanistic models, identifying five constraints which guide the articulation of models in molecular systems biology. These constraints are not independent of one another, with the result that modeling becomes an iterative process. We illustrate the use of these constraints in the modeling of the mechanism for bistability in the lac operon. (shrink)

Traditional approaches to theory structure and theory change in science do not fare well when confronted with the practice of certain fields of science. We offer an account of contemporary practice in molecular biology designed to address two questions: Is theory change in this area of science gradual or saltatory? What is the relation between molecular biology and the fields of traditional biology? Our main focus is a recent episode in molecular biology, the (...) discovery of enzymatic RNA. We argue that our reconstruction of this episode shows that traditional approaches to theory structure and theory change need considerable refinement if they are to be defended as generally applicable. 1This paper emerged from discussions between us, and we are both equally responsible for its errors. We would like to thank Yvonne Paterson for helpful comments. (shrink)

The comprehension of living organisms in all their complexity poses a major challenge to the biological sciences. Recently, systems biology has been proposed as a new candidate in the development of such a comprehension. The main objective of this paper is to address what systems biology is and how it is practised. To this end, the basic tools of a systems biological approach are explored and illustrated. In addition, it is questioned whether systems biology ‘revolutionizes’ molecular (...) biology and ‘transcends’ its assumed reductionism. The strength of this claim appears to depend on how molecular and systems biology are characterised and on how reductionism is interpreted. Doing credit to molecular biology and to methodological reductionism, it is argued that the distinction between molecular and systems biology is gradual rather than sharp. As such, the classical challenge in biology to manage, interpret and integrate biological data into functional wholes is further intensified by systems biology’s use of modelling and bioinformatics, and by its scale enlargement. (shrink)

Since the 1930s, scientists studying the neurological disease scrapie had assumed that the infectious agent was a virus. By the mid 1960s, however, several unconventional properties had arisen that were difficult to reconcile with the standard viral model. Evidence for nucleic acid within the pathogen was lacking, and some researchers considered the possibility that the infectious agent consisted solely of protein. In 1982, Stanley Prusiner coined the term `prion' to emphasize the agent's proteinaceous nature. This infectious protein hypothesis was denounced (...) by many scientists as `heretical'.This essay asks why the concept of an infectious protein was considered controversial. Some biologists justified their evaluation of this hypothesis on the grounds that an infectious protein contradicted the `central dogma of molecular biology'. Others referred to vague theoretical constraints such as molecular biology's `theoretical structure' or `framework'. Examination of the objections raised by researchers reveals exactly what generalizations were being challenged by a protein model of infection.This two-part survey of scrapie and prion research reaches several conclusions: (1) A theoretical framework is present in molecular biology, exerting its influence in hypothesis formation and evaluation; (2) This framework consists of several related, yet separable, generalizations or `elements', including Francis Crick's Central Dogma and Sequence Hypothesis, plus notions concerning infection, replication, protein synthesis, and protein folding; (3) The term `central dogma' has stretched beyond Crick's original 1958 definition to encompass at least two other `framework elements': replication and protein synthesis; and (4) From the study of scrapie and related diseases, biological information has been delineated into at least two classes: sequential and what I call `conformational'.In Part I of this essay, a brief review of the central dogma, as outlined by both Francis Crick and James Watson, will be given. The developments in scrapie research from 1965 to 1972 will then be traced. This section will summarize many of the puzzling, non-viral-like properties of the scrapie agent. Alternative hypotheses to the viral explanation will also be presented, including early versions of a protein-only hypothesis. Part II of this essay will follow the developments in scrapie and prion research from the mid 1970s through 1991. The growing prominence of a protein-only model of infection will be balanced by continued objections from many researchers to a pathogen devoid of nucleic acid. These objections will help illuminate those generalizations in molecular biology that were indeed challenged by a protein-only model of infection. (shrink)

An assessment is offered of the recent debate on information in the philosophy of biology, and an analysis is provided of the notion of information as applied in scientific practice in molecular genetics. In particular, this paper deals with the dependence of basic generalizations of molecular biology, above all the ‘central dogma’, on the so-called ‘informational talk’ (Maynard Smith [2000a]). It is argued that talk of information in the ‘central dogma’ can be reduced to causal claims. (...) In that respect, the primary aim of the paper is to consider a solution to the major difficulty of the causal interpretation of genetic information: how to distinguish the privileged causal role assigned to nucleic acids, DNA in particular, in the processes of replication and protein production. A close reading is proposed of Francis H. C. Crick's On Protein Synthesis (1958) and related works, to which we owe the first explicit definition of information within the scientific practice of molecular biology. Introduction 1.1 The basic questions of the information debate 1.2 The causal interpretation (CI) of biological information and Crick's ‘central dogma’ Crick's definitions of genetic information The main requirement for (CI) Types of causation in molecular biology 4.1 Structural causation in molecular biology 4.2 Nucleic acids as correlative causal factors The ‘central dogma’ without the notion of information Concluding remarks This is a new version of this article as there were errors in the abstract and full text in the previous version. (shrink)

The increasing place of evolutionary scenarios in functional biology is one of the major indicators of the present encounter between evolutionary biology and functional biology (such as physiology, biochemistry and molecular biology), the two branches of biology which remained separated throughout the twentieth century. Evolutionary scenarios were not absent from functional biology, but their places were limited, and they did not generate research programs. I compare two examples of these past scenarios with two (...) present-day ones. At least three characteristics distinguish present and past efforts: An excellent description of the systems under study, a rigorous use of the evolutionary models, and the possibility to experimentally test the evolutionary scenarios. These three criteria allow us to distinguish the domains in which the encounter is likely to be fruitful, and those where the obstacles to be overcome are high and in which the proposed scenarios have to be considered with considerable circumspection. (shrink)

An exploration of the nexus between ecology, evolutionary biology and molecular biology, via the concept of phenotypic plasticity.

This paper is devoted to an examination of the discovery, characterization, and analysis of the functions of microRNAs, which also serves as a vehicle for demonstrating the importance of exploratory experimentation in current (post-genomic) molecular biology. The material on microRNAs is important in its own right: it provides important insight into the extreme complexity of regulatory networks involving components made of DNA, RNA, and protein. These networks play a central role in regulating development of multicellular organisms and illustrate (...) the importance of epigenetic as well as genetic systems in evolution and development. The examination of these matters yields principled arguments for the historicity of the functions of key biological molecules and for the indispensability of exploratory experimentation in contemporary molecular biology as well as some insight into the complex interplay between exploratory experimentation and hypothesis-driven science. This latter result is not only of importance for philosophy of science, but also of practical importance for the evaluation of grant proposals, although the elaboration of this latter claim must be left for another occasion. (shrink)

The “DNA is a program” metaphor is still widely used in Molecular Biology and its popularization. There are good historical reasons for the use of such a metaphor or theoretical model. Yet we argue that both the metaphor and the model are essentially inadequate also from the point of view of Physics and Computer Science. Relevant work has already been done, in Biology, criticizing the programming paradigm. We will refer to empirical evidence and theoretical writings in (...) class='Hi'>Biology, although our arguments will be mostly based on a comparison with the use of differential methods (in Molecular Biology: a mutation or alike is observed or induced and its phenotypic consequences are observed) as applied in Computer Science and in Physics, where this fundamental tool for empirical investigation originated and acquired a well-justified status. In particular, as we will argue, the programming paradigm is not theoretically sound as a causal(as in Physics) or deductive(as in Programming) framework for relating the genome to the phenotype, in contrast to the physicalist and computational grounds that this paradigm claims to propose. (shrink)

I defend the view that single experiments can provide a sufficient reason for preferring one among a group of hypotheses against the widely held belief that “crucial experiments” are impossible. My argument is based on the examination of a historical case from molecular biology, namely the Meselson-Stahl experiment. “The most beautiful experiment in biology”, as it is known, provided the first experimental evidence for the operation of a semi-conservative mechanism of DNA replication, as predicted by Watson and (...) Crick in 1953. I use a mechanistic account of explanation to show that this case is best construed as an inference to the best explanation (IBE). Furthermore, I show how such an account can deal with Duhem's well-known arguments against crucial experiments as well as Van Fraassen's “bad lot” argument against IBE. (shrink)

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

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)

The applicability of Nagel's concept of theory reduction, and related concepts of reduction, to the reduction of genetics to molecular biology is examined using the lactose operon in Escherichia coli as an example. Geneticists have produced the complete nucleotide sequence of two of the genes which compose this operon. If any example of reduction in genetics should fit Nagel's analysis, the lactose operon should. Nevertheless, Nagel's formal conditions of theory reduction are inapplicable in this case. Instead, it is (...) argued that genetics has been partially reduced to molecular biology in the sense of token-token reduction. (shrink)

A recurrent theme in ethnomethodological research is that of instructed actions. Contrary to the classic traditions in the social and cognitive sciences, which attribute logical priority or causal primacy to instructions, rules, and structures of action, ethnomethodologists investigate the situated production of actions which enable such formulations to stand as adequate accounts. Consequently, a recitation of formal structures can not count as an adequate sociological description, when no account is given of the local production ofwhat those structures describe. The natural (...) sciences can be described as a domain of practical action in whichthe use of methods enables the intersubjective reproduction of naturalistic observations and experiments. As numerous sociological studies of laboratory practices have shown, the achievement of intersubjective order cannot be reduced to formal methods; instead, it arises from the work of custom-fitting relevant methods to the local circumstances of the research. In this paper we discuss a possible extension of this idea to cover two intertwined aspects of molecular biology: (1) the work of following instructions on how to perform routine laboratory procedures, and (2) the relationship between cellular orders and the encoded instructions contained in the DNA molecule. We suggest that a classic conception of scientific action is implied by the way formal instructions are treated as a primary basis, both for molecular biologists' actions and the cellular functions they study, and we envision an ethnomethodological alternative to those conceptions of social and biological order. (shrink)

Until the 1930s Germany had been the international leader in biochemistry, chemistry, and areas of biology. After WWII, however, molecular biology as a new interdisciplinary scientific enterprise was scarcely represented in Germany for almost 20 years. Three major reasons for the low performance of molecular biology are discussed: first, the forced emigration of Jewish scientists after 1933, which not only led to the expulsion of future distinguished molecular biologists, but also to a strong decline (...) of ''dynamic biochemistry'', a field which contributed greatly to molecular biology. Second, German university structures that strongly impeded interdisciplinary research. Third, the international isolation and self-isolation of German scientists that was a major obstacle to the implementation of new fields of research developed elsewhere. Despite the fact that there was no official boycott against Germany as there had been after WWI and despite the Cold War policy of integrating Germans into the West, as a consequence of National Socialism and WWI for many years only very few German scientists gained access to the international community of molecular biologists. Max Delbruck played an important role in helping the Germans establish modern, mostly molecular, biology because he retained strong connections to Germany. Most importantly, it required a new generation of young scientists who had received part of their training in the US to establish modern molecular biology at German universities and Max Planck Institutes. (shrink)

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

This article examines how a molecular "solution" to an important biological problem-how is antibody diversity generated? was obtained in the 1970s. After the primarily biological clonal selection theory (CST) was accepted by 1967, immunologists developed several different contrasting theories to complete the SCST. To choose among these theories, immunology had to turn to the new molecular biology, first to nucleic acid hybridization and then to recombinant DNA technology. The research programs of Tonegawa and Leder that led to (...) the "solution" are discussed, and some of their strategies and heuristics are broadly characterized: (1) to what extent does the new recombinant DNA technology provide what the scientists claim is "direct evidence," what does that term mean, and what are the implications of that claim for biological "realism," and (2) is this episode one of reduction, partial reduction, or explanatory extension, and what do these terms mean in the context of a successful molecular "solution" to a biological problem. (shrink)

An assessment is offered of the recent debate on information in the philosophy of biology, and an analysis is provided of the notion of information as applied in scientific practice in molecular genetics. In particular, this paper deals with the dependence of basic generalizations of molecular biology, above all the 'central dogma', on the socalled 'informational talk' (Maynard Smith [2000a]). It is argued that talk of information in the 'central dogma' can be reduced to causal claims. (...) In that respect, the primary aim of the paper is to consider a solution to the major difficulty of the causal interpretation of genetic information: how to distinguish the privileged causal role assigned to nucleic acids, DNA in particular, in the processes of replication and protein production. A close reading is proposed of Francis H. C. Crick's On Protein Synthesis ([1958]) and related works, to which we owe the first explicit definition of information within the scientific practice of molecular biology. (shrink)

The Medical Research Council Laboratory of Molecular Biology (formerly the Medical Research Council Unit for the Study of Molecular Structure of Biological Systems) in Cambridge (England) played a key role in the postwar history of molecular biology. The paper, focussing on the early history of the institution, aims to show that the creation of the laboratory and the making of molecular biology were part of a new scientific culture set in place after World (...) War II. In five interlinked parts it deals with the institutional creation of the MRC unit dedicated to the crystallographic analysis of biological molecules; the attraction of postwar biophysics, the heading under which the work of the unit initially fell; the people who joined the laboratory and their appropriation of new technologies, in particular the electronic computer for protein crystal structure determination; the cultural appeal of postwar crystallography, as exemplified in the use of crystal structure diagrams for a wide series of consumer goods at the Festival of Britain in 1951 and the display of molecular models at the Brussels World's Fair in 1958, a key site for the presentation of science and its role in the postwar world. (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)

RESUMEN: Abir-Am ha criticado la visión estándar de que la Fundación Rockefeller (FR) jugó un papel central en el surgimiento de la biología molecular durante la década de 1960. En su opinión, la FR aceleró la molecularización de las ciencias de la vida, pero no intervino de manera directa en el surgimiento de la biología molecular como disciplina. Aquí sostengo que esta crítica tiene consecuencias mayores a las que sospechó su autora y muestro que la tesis de la (...) centralidad de la FR en el desarrollo de la biología molecular no se puede desmantelar sin alterar también la visión de la biologia molecular como una disciplina orientada a la resolución de problemas predefinidos.ABSTRACT: Abir-Am has critiqued the standard view that the Rockefeller Foundation (RF) played a central role in the development of molecular biology during the 1960s. In her view, the RF accelerated the molecularization of the life sciences, but it did not directly contribute to building molecular biology’s disciplinary identity. Here I argue that Abir-Am’s critique has more consequences than she envisioned, and I show that the thesis of the centrality of the RF cannot be dismantled without also altering the view of molecular biology as a field oriented towards the solution of predefined problems. (shrink)

From the mid-1960s onwards, a set of Spanish molecular biology research groups emerged in Spain. The factors contributing to this included: the return of a group of molecular biologists from their postdoctoral period abroad, the negotiations for the return of Spanish-born Nobel prize winner Severo Ochoa from New York, the negotiations for Spanish membership in the European Conference of Molecular Biology, and national policy towards university reform. As a result, the early molecular biologists' research (...) groups began to be recognised as research schools by Spanish authorities and postgraduate courses and new research centres for molecular biology were set up. Foreign influence in the whole process was crucial. (shrink)

The present paper analyzes the use and understanding of the homology concept across different biological disciplines. It is argued that in its history, the homology concept underwent a sort of adaptive radiation. Once it migrated from comparative anatomy into new biological fields, the homology concept changed in accordance with the theoretical aims and interests of these disciplines. The paper gives a case study of the theoretical role that homology plays in comparative and evolutionary biology, in molecular biology, (...) and in evolutionary developmental biology. It is shown that the concept or variant of homology preferred by a particular biological field is used to bring about items of biological knowledge that are characteristic for this field. A particular branch of biology uses its homology concept to pursue its specific theoretical goals. (shrink)

This paper, which is based on recent empirical research at the University of Leeds, the University of Edinburgh, and the University of Bristol, presents two difficulties which arise when condensed matter physicists interact with molecular biologists: (1) the former use models which appear to be too coarse-grained, approximate and/or idealized to serve a useful scientific purpose to the latter; and (2) the latter have a rather narrower view of what counts as an experiment, particularly when it comes to computer (...) simulations, than the former. It argues that these findings are related; that computer simulations are considered to be undeserving of experimental status, by molecular biologists, precisely because of the idealizations and approximations that they involve. The complexity of biological systems is a key factor. The paper concludes by critically examining whether the new research programme of ‘systems biology’ offers a genuine alternative to the modelling strategies used by physicists. It argues that it does not. (shrink)

The theory of concepts advanced in the dissertation aims at accounting for a) how a concept makes successful practice possible, and b) how a scientific concept can be subject to rational change in the course of history. Traditional accounts in the philosophy of science have usually studied concepts in terms only of their reference; their concern is to establish a stability of reference in order to address the incommensurability problem. My discussion, in contrast, suggests that each scientific concept consists of (...) three components of content: 1) reference, 2) inferential role, and 3) the epistemic goal pursued with the concept's use. I argue that in the course of history a concept can change in any of these three components, and that change in one component—including change of reference—can be accounted for as being rational relative to other components, in particular a concept's epistemic goal. This semantic framework is applied to two cases from the history of biology: the homology concept as used in 19th and 20th century biology, and the gene concept as used in different parts of the 20th century. The homology case study argues that the advent of Darwinian evolutionary theory, despite introducing a new definition of homology, did not bring about a new homology concept (distinct from the pre-Darwinian concept) in the 19th century. Nowadays, however, distinct homology concepts are used in systematics/evolutionary biology, in evolutionary developmental biology, and in molecular biology. The emergence of these different homology concepts is explained as occurring in a rational fashion. The gene case study argues that conceptual progress occurred with the transition from the classical to the molecular gene concept, despite a change in reference. In the last two decades, change occurred internal to the molecular gene concept, so that nowadays this concept's usage and reference varies from context to context. I argue that this situation emerged rationally and that the current variation in usage and reference is conducive to biological practice. The dissertation uses ideas and methodological tools from the philosophy of mind and language, the philosophy of science, the history of science, and the psychology of concepts. (shrink)

Current accounts of the relationship between classical genetics and molecular biology favor the ‘explanatory extension’ thesis, according to which molecular biology elucidates aspects of inheritance unexplained by classical genetics. I identify however an unresolved tension between the ‘explanatory extension’ account and examples of ‘explanatory interference’ (cases when the accommodation of data from molecular biology results in a more precise genotyping and more adequate classical explanations). This paper provides a new way of analyzing the relationship (...) between classical genetics and molecular biology capable of resolving this tension. The proposed solution makes use of the properties of mechanism schemas and sketches, which can be completed by elucidating some or all of their remaining ‘black boxes’ and instantiated via the filling-in of phenomenon-specific details. This result has implications for the reductionism -antireductionism debate since it shows that molecular elucidations have a positive impact on classical explanations without entailing the reduction of classical genetics to molecular biology. (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)

“I myself was forced to call myself a molecular biologist because when inquiring clergymen asked me what I did, I got tired of explaining that I was a mixture of crystallographer, biophysicist, biochemist, and geneticist.” Thus explained Francis Crick, who with James Watson discovered in 1953 the double helical structure of DNA, the genetic material..

Molecular biologists use different kinds of reasoning strategies for different tasks, such as hypothesis formation, experimental design, and anomaly resolution. More specifically, the reasoning strategies discussed in this paper may be characterized as (1) abstraction-instantiation, in which an abstract skeletal model is instantiated to produce an experimental system; (2) the systematic scan, in which alternative hypotheses are systematically generated; and (3) modular anomaly resolution, in which components of a model are stated explicitly and methodically changed to generate alternative changes (...) to resolve an anomaly. This work grew out of close observation over a period of six months of an actively functioning molecular genetics laboratory. (shrink)

Although molecular biology has meant different things at different times, the term is often associated with a tendency to view cellular causation as conforming to simple linear schemas in which macro-scale effects are specified by micro-scale structures. The early achievements of molecular biologists were important for the formation of such an outlook, one to which the discovery of recombinant DNA techniques, and a number of other findings, gave new life even after the complexity of genotype–phenotype
relations had become (...) apparent. Against this background we outline how a range of scientific developments and conceptual considerations can be regarded as enabling and perhaps necessitating contemporary systems approaches. We suggest that philosophical ideas have a valuable part to play in making sense of complex scientific and disciplinary issues. (shrink)

This paper provides an account of the experimental conditions required for establishing whether correlating or causally relevant factors are constitutive components of a mechanism connecting input (start) and output (finish) conditions. I argue that two-variable experiments, where both the initial conditions and a component postulated by the mechanism are simultaneously manipulated on an independent basis, are usually required in order to differentiate between correlating or causally relevant factors and constitutively relevant ones. Based on a typical research project molecular (...) class='Hi'>biology, a flowchart model detailing typical stages in the formulation and testing of hypotheses about mechanistic components is also developed. (shrink)

Rather than starting with traits and speculating whether selective forces drove evolution in past environments, we propose starting with a candidate gene associated with a trait and testing first for patterns of selection at the DNA level. This can provide limitations on the number of traits to be evaluated subsequently by adaptationism as described by Andrews et al.

In this thesis I examine a number of topics that bear on explanation and understanding in molecular and cell biology, in order to shed new light on explanatory practice in those areas and to find novel angles from which to approach relevant philosophical debates. The topics I look at include mechanism, emergence, cellular complexity, and the informational role of the genome. I develop a perspective that stresses the intimacy of the relations between ontology and epistemology. Whether a phenomenon (...) looks mechanistic, or complex, or indeed emergent, is largely an epistemic matter, yet has an objective basis in features of the world. After reviewing several concepts of mechanism I consider the influential recent account of Machamer, Darden and Craver (MDC). That account makes interesting proposals concerning the relationship between mechanistic explanation and intelligibility, which are consistent with the results of the investigation I undertake into the science surrounding protein folding. In relation to a number of other issues pertaining to biological systems I conclude that the MDC account is insufficiently nuanced, however, leading me to outline an alternative approach to mechanism. This emphasizes the importance of structure—function relations and addresses issues raised by reflection on the nature of cellular complexity. These include the distinction between structure and process and the different possible bases on which system organization may be maintained. The account I give of emergence construes the phenomenon in terms of psychological deficit: phenomena are emergent when we lack the capacity to trace through and model their causal structures using our cognitive schemas. I conclude by developing these ideas into a preliminary and partial account of explanation and understanding. This aspires to cover the significant fraction of work in molecular and cell biology that correlates biological structures, processes and functions by visualizing phenomena and making them imaginable. (shrink)

This paper argues in defense of theanti-reductionist consensus in the philosophy ofbiology. More specifically, it takes issues with AlexRosenberg's recent challenge of this position. Weargue that the results of modern developmentalgenetics rather than eliminating the need forfunctional kinds in explanations of developmentactually reinforce their importance.

In this paper I use a case study—the discovery of the chaperon function exerted by proteins in the various steps of the hereditary process—to re-discuss the question whether the nucleic acids are the sole repositories of relevant information as assumed in the information theory of heredity. The evidence I here present of a crucial role for molecular chaperones in the folding of nascent proteins, as well as in DNA duplication, RNA folding and gene control, suggests that the family of (...) proteins acting as molecular chaperones provides information that is complementary to that stored in the nucleic acids, and equally important. A re-evaluation of the role of proteins in the hereditary process is in order away from the gene-centric approach of the information theory of heredity, to which neo-Darwinian evolutionists adhere. (shrink)

In a spellbinding narrative that skillfully weaves together cutting-edge research among today's foremost scientists, theoretical physicist Michio Kaku--author of the bestselling book Hyperspace --presents a bold, exhilarating adventure into the science of tomorrow. In Visions, Dr. Kaku examines in vivid detail how the three scientific revolutions that profoundly reshaped the twentieth century--the quantum, biogenetic, and computer revolutions--will transform the way we live in the twenty-first century. The fundamental elements of matter and life--the particles of the atom and the nucleus of (...) the cell--have now been decoded, closing one of the great chapters of scientific history. But this is just the preface to an even more far-reaching scientific revolution, as we make the transition from being passive observers of the mysteries of nature to becoming masters of nature, able to manipulate matter, life, and intelligence to remold the world around us. In the first part of Visions, Dr. Kaku discusses the cyber future, when millions of microprocessors are scattered throughout our environment; when the iron principle that has ruled the computer industry, Moore's Law, finally collapses, forcing scientists to adopt startling new designs like DNA computers and quantum computers; and when artificial intelligence systems finally arrive. In the next section, Dr. Kaku shows how the decoding of DNA will allow us to conquer devastating genetic diseases, defeat many cancers at the molecular level, synthesize new medicines using virtual reality, grow new organs, conquer aging and reshape our genetic inheritance. Finally, he explores how quantum physicists will perfect new ways to harness the cosmic energy of the universe--from molecular machines to supermagnets that may energize a second industrial revolution, to powerful fusion engines that one day may take us to the stars. What makes Michio Kaku's vision of the future of science so compelling and authoritative is that it is based on the groundbreaking research already underway at leading laboratories around the world. Weaving interviews with over 150 scientists--several of them Nobel laureates--into a rich, inspiring narrative, Dr. Kaku reveals the growing consensus among key scientists about how science will likely evolve through the early, middle, and late years of the twenty-first century. An intimate, thrilling tour through the next century of science, Visions is a riveting, essential map to how scientists will reshape our future. (shrink)

‘‘Theoretical biology’’ is a surprisingly heter- ogeneous field, partly because it encompasses ‘‘doing the- ory’’ across disciplines as diverse as molecular biology, systematics, ecology, and evolutionary biology. Moreover, it is done in a stunning variety of different ways, using anything from formal analytical models to computer sim- ulations, from graphic representations to verbal arguments. In this essay I survey a number of aspects of what it means to do theoretical biology, and how they compare with (...) the allegedly much more restricted sense of theory in the physical sciences. I also tackle a recent trend toward the presentation of all-encompassing theories in the biological sciences, from general theories of ecology to a recent attempt to provide a conceptual framework for the entire set of biological disciplines. Finally, I discuss the roles played by philosophers of science in criticizing and shap- ing biological theorizing. (shrink)

In behavioral ecology some authors regard the innateness concept as irretrievably confused whilst others take it to refer to adaptations. In cognitive psychology, however, whether traits are 'innate' is regarded as a significant question and is often the subject of heated debate. Several philosophers have tried to define innateness with the intention of making sense of its use in cognitive psychology. In contrast, I argue that the concept is irretrievably confused. The vernacular innateness concept represents a key aspect of 'folkbiology', (...) namely, the explanatory strategy that psychologists and cognitive anthropologists have labeled 'folk essentialism'. Folk essentialism is inimical to Darwinism, and both Darwin and the founders of the modern synthesis struggled to overcome this way of thinking about living systems. Because the vernacular concept of innateness is part of folkbiology, attempts to define it more adequately are unlikely to succeed, making it preferable to introduce new, neutral terms for the various, related notions that are needed to understand cognitive development. (shrink)

Physicalism and antireductionism are the ruling orthodoxy in the philosophy of biology. But these two theses are difficult to reconcile. Merely embracing an epistemic antireductionism will not suffice, as both reductionists and antireductionists accept that given our cognitive interests and limitations, non-molecular explanations may not be improved, corrected or grounded in molecular ones. Moreover, antireductionists themselves view their claim as a metaphysical or ontological one about the existence of facts molecular biology cannot identify, express, or (...) explain. However, this is tantamount to a rejection of physicalism and so causes the antireductionist discomfort. In this paper we argue that vindicating physicalism requires a physicalistic account of the principle of natural selection, and we provide such an account. The most important pay-off to the account is that it provides for the very sort of autonomy from the physical that antireductionists need without threatening their commitment to physicalism. (shrink)

John Dupré explores recent revolutionary developments in biology and considers their relevance for our understanding of human nature and human society. Epigenetics and related areas of molecular biology have eroded the exceptional status of the gene and presented the genome as fully interactive with the rest of the cell. Developmental systems theory provides a space for a vision of evolution that takes full account of the fundamental importance of developmental processes. Dupré shows the importance of microbiology for (...) a proper understanding of the living world, and reveals how it subverts such basic biological assumptions as the organisation of biological kinds on a branching tree of life, and the simple traditional conception of the biological organism. -/- These topics are considered in the context of a view of science as realistically grounded in the natural order, but at the same time as pluralistic and inextricably integrated within a social and normative context. The volume includes a section that recapitulates and expands some of the author's general views on science; a section addressing a range of topics in biology, including the significance of genomics, the nature of the organism and the current status of evolutionary theory; and a section exploring some implications of contemporary biology for humans, for example on the reality or unreality of human races, and the plasticity of human nature. (shrink)

One important aspect of biological explanation is detailed causal modeling of particular phenomena in limited experimental background conditions. Recognising this allows a new avenue for intertheoretic reduction to be seen. Reductions in biology are possible, when one fully recognises that a sufficient condition for a reduction in biology is a molecular model of 1) only the demonstrated causal parameters of a biological model and 2) only within a replicable experimental background. These intertheoretic identifications –which are ubiquitous in (...) biology and form the basis of ruthless reductions (Bickle 2003)- are criticised as merely “local” (Sullivan 2009) or “fragmentary” (Schaffner 2006). However, in an instructive case, a biological model is preserved in molecular terms, and a complex biological phenomenon has been successfully reduced. In doing this the molecular model remains valid in a broader range of background conditions and meaningfully unites disparate biological phenomena. (shrink)

On the nature-nurture debate and the complexities of what make us human.

Comprised of essays by top scholars in the field, this volume offers concise overviews of philosophical issues raised by biology. Brings together a team of eminent scholars to explore the philosophical issues raised by biology Addresses traditional and emerging topics, spanning molecular biology and genetics, evolution, developmental biology, immunology, ecology, mind and behaviour, neuroscience, and experimentation Begins with a thorough introduction to the field Goes beyond previous treatments that focused only on evolution to give equal (...) attention to other areas, such as molecular and developmental biology Represents both an authoritative guide to philosophy of biology, and an accessible reference work for anyone seeking to learn about this rapidly-changing field. (shrink)

Systems Biology and the Modern Synthesis are recent versions of two classical biological paradigms that are known as structuralism and functionalism, or internalism and externalism. According to functionalism (or externalism), living matter is a fundamentally passive entity that owes its organization to external forces (functions that shape organs) or to an external organizing agent (natural selection). Structuralism (or internalism), is the view that living matter is an intrinsically active entity that is capable of organizing itself from within, with purely (...) internal processes that are based on mathematical principles and physical laws. At the molecular level, the basic mechanism of the Modern Synthesis is molecular copying, the process that leads in the short run to heredity and in the long run to natural selection. The basic mechanism of Systems Biology, instead, is self-assembly, the process by which many supramolecular structures are formed by the spontaneous aggregation of their components. In addition to molecular copying and self-assembly, however, molecular biology has uncovered also a third great mechanism at the heart of life. The existence of the genetic code and of many other organic codes in Nature tells us that molecular coding is a biological reality and we need therefore a framework that accounts for it. This framework is Code biology, the study of the codes of life, a new field of research that brings to light an entirely new dimension of the living world and gives us a completely new understanding of the origin and the evolution of life. (shrink)

An eminent neurobiologist reflects on the human brain, connecting recent scientific findings with ideas from an array of other disciplines.

One important aspect of biological explanation is detailed causal modeling of particular phenomena in limited experimental background conditions. Recognising this allows one to appreciate that a sufficient condition for a reduction in biology is a molecular model of (1) only the demonstrated causal parameters of a biological model and (2) only within a replicable experimental background. These identities—which are ubiquitous in biology and form the basis of ruthless reductions (Bickle, Philosophy and neuroscience: a ruthlessly reductive account, 2003)—are (...) criticised as merely “local” (Sullivan, Synthese 167:511–539, 2009) or “fragmentary” (Schaffner, Synthese, 151(3):377–402, 2006). However, in an instructive case, a biological model is preserved in molecular terms, demonstrating a complex phenomenon that has been successfully reduced. (shrink)

Are living organisms--as Descartes argued--just machines? Or is the nature of life such that it can never be fully explained by mechanistic models? In this thought-provoking and controversial book, eminent geophysicist Walter M. Elsasser argues that the behavior of living organisms cannot be reduced to physico-chemical causality. Suggesting that molecular biology today is at the same point as Newtonian physics on the eve of the quantum revolution, Elsasser lays the foundation for a theoretical biology that points the (...) way toward a natural philosophy of organic life. Explicitly repudiating "vitalism" (the notion that the laws of nature need to be modified when applied to living organisms), Elsasser argues instead that the structural complexity of even a single living cell is "transcomputational"--that is, beyond the power of any imaginable system to compute. Beginning from this insight, Elsasser leads the reader through a step-by-step process that ultimately arrives at the conclusion that living and non-living matter are separated by "a no-man's land of irrationality." Trained in Germany as a physicist, Elsasser first pondered the implications of quantum mechanics for biology as early as 1951. The more closely he studied the inherent complexity of life, the more skeptical he became of the reductionist view of organisms as tiny machines. "An organism," he concluded, "is a source of causal chains which cannot be traced beyond a terminal point because they are lost in the unfathomable complexity of the organism." Like the physicist who works within the bounds of an unfathomable universe, Elsasser argues, the biologist must seek answers within a system that is no less unfathomable. (shrink)