The Post-genomic Era includes features both from a methodological and epistemic point of view and from an ontological perspective. Firstly, it incorporates new methods of high-throughput sequencing of DNA and RNA, and the development of complete genomes that allow a precise reference of the molecular results obtained. In addition, from an ontological perspective, the centre of gravity of the molecular processes is placed on the expression of genes, and the way in which such expression is regulated; these features turn the (...) attention towards the study of Gene Regulatory Networks, and in particular to the role of RNA. This new molecular-biological perspective based on new methodologies and approaches is affecting the existing Molecular Genetics Theory including the definition of gen and Central Dogma of Molecular Biology. An important philosophical challenges posed by this new situation is the question whether there is a sophistication of the present theory or a New Theory of Molecular Genetics and whether there is an incommensurability between this theory and the accepted theory. In this work we evaluate these changes in the light of Kuhn’s theory of scientific revolution in order to propose an alternative between a moderate and a strong view. According to the moderate one, the Post-genomic changes do not properly involve a paradigm shift or, if they do, they constitute a minor revolution. The strong view considers that, the anomalies disclosed in the Molecular Genetics Theory at conceptual and methodological level and the Post-genomic changes they lead to suppose a scientific paradigm shift. (shrink)

In this paper, it is argued that, contrary to some suggestions in the philosophical literature, dispositions cannot replace laws in the description of the physical world. If for a certain type of physical situation a well-working law-based account is available, then it is not possible to describe that situation equally well in terms of dispositions. Using an example consisting of four laws (Coulomb’s law, Newton’s law of gravitation, the rule for the composition of forces and Newton’s second law), it is (...) shown that when one attempts to replace a law-based account with a disposition-based account, the latter turns out to be either less informative or inferior with respect to theoretical virtues, such as simplicity, unification, non-triviality of predictions and explanatory power. Laws are also better suited to deal with interactions and their screening off. Using inference to the best explanation, one can conclude from this comparison that it is laws rather than dispositions that should be included in our ontological picture of nature. (shrink)

Using the context of controversies surrounding evolutionary developmental biology (EvoDevo) and the possibility of an Extended Evolutionary Synthesis, I provide an account of theory structure as idealized theory presentations that are always incomplete (partial) and shaped by their conceptual content (material rather than formal organization). These two characteristics are salient because the goals that organize and regulate scientific practice, including the activity of using a theory, are heterogeneous. This means that the same theory can be structured differently, in part because (...) theory presentations (as idealizations) intentionally depart from different features known to be present in a theory. Since there are diverse and potentially incompatible theory structures derived from heterogeneous goals found in scientific practices, a question arises about the absence of a unifying theory structure in the background. The notion of a “theory façade” offers a fruitful perspective on this potentially unsettling result. (shrink)

The aim of this article is to discuss and develop the diagnose of the Hardy-Weinberg law made by van Fraassen (1987, p. 110), according to which: 1) that law cannot be considered a law used as an axiom for the classical population genetics as a whole, since it is an equilibrium-law that holds only under certain special conditions; 2) it just determines a subclass of models; 3) its generalization shades off into logical vacuity; and 4) more complex variants of the (...) law can be deduced for more realistic assumptions. The discussion and development of such a diagnose will be carried out with the notions of another semantic conceptions of theories, related to that of van Fraassen, namely, the structuralist view of theories, and a rational reconstruction of classical population genetics made within the framework of such a metatheory, also presented in this paper. (shrink)

I admire Wilson & Sober's (W & S's) aim, to alert social scientists that group selection has risen from the ashqs, and to explicate its relevance to the behavioral sciences. Group selection has beenwidely misunderstood; furthermore, both authors have been instrumental in illuminating conceptual problems surrounding higher-level selection. Still, I find that this target article muddies the waters, primarily through its shifting and confused definition of a "vehicle" of selection. The fundamental problem is an ambiguity in the definition of "adaptation." (...) On the one hand, any evolutionary change that results from a selection process could be called an adaptation, by definition; I call this the "weak" view of adaptation. A "strong" view of adaptation, on the other hand, includes some notion of design - the evolution of a specific complex trait understood, in an engineering sense, to provide a mechanism favoring its owner's success in contributing to the evolutionary lineage. (shrink)

Recently, several critics of the multiple realizability thesis have argued that philosophers have tended to accept the thesis on too weak grounds. On the one hand, the analytic challenge has problematized how philosophers have treated the multiple realization relation itself, claiming that assessment of the sameness of function and the relevant difference of realizers has been uncritical. On the other hand, it is argued that the purported evidence of the thesis is often left empirically unverified. This paper provides a novel (...) strategy to answer these worries by introducing a role for multiple realizability in the context of biological engineering. In the field of synthetic biology, bioengineers redesign the evolutionary realizations of biological functions, even constructing artificial chemical surrogates in the laboratory. I show how in the rational design approach to biological engineering, multiple realizability can function as a design heuristic in which the sameness of function and difference of realizers can be controlled. Although practically motivated, this engineering approach has also a theoretical, exploratory component that can be used to study the empirical limitations of multiple realizability. Successful realization of the engineering designs would amount to a concrete demonstration of multiple realizability, taking evidence for MRT beyond what is readily found in nature. (shrink)

Description of the biologicalhierarchy of the organism has been extendedhere to included the evolutionary andecological sub-hierarchies with theirrespective levels in order to give a completehierarchical description of life. These newdescriptions include direction of formation,types of constraints, and dual levels. Constraints are produced at the macromolecularlevel of genes/proteins, some of which (a) aredescendent restraints which hold a hierarchytogether and others (b) interact horizontallywith selective agents at corresponding levelsof the niche. The organism is a dual levelconstrained by both the ecologicalsub-hierarchy (survival) and (...) evolutionarysub-hierarchy (fitness) while serving as thehighest level of the specializationsub-hierarchy, therefore, it is unique inbelonging to three sub-hierarchies. Organismsexperience birth, sometimes death, andparticipate in evolution. Birth of an organismis realized when a cell is removed from theconstraints of the organism and assumes itsown organismal constraints. Death occurs withthe cessation of protein synthesis becauseproteins and their products constitutecomponents at high levels of the hierarchy. Selection is of two types, natural selection,involving adaptive traits interacting withfeatures in a niche, and hierarchicalselection, requiring traits to be compatiblewith existing hierarchical constraints. (shrink)

This paper explores the explanatory adequacy of lower-level theories when their higher-level counterparts are irreducible. If some state or entity described by a high-level theory supervenes upon and is realized in events, entities, etc. described by the relevant lower-level theory, does the latter fully explain the higher-level event even if the higher-level theory is irreducible? While the autonomy of the special sciences and the success of various eliminativist programs depends in large part on how we answer this question, neither the (...) affirmative or negative answer has been defended in detail. I argue, contra Putnam and others, that certain facts about causation and explanation show that such lower-level theories do explain. I also argue, however, that there may be important questions about counterfactuals and laws that such explanations cannot answer, thereby showing their partial inadequacy. I defend the latter claim against criticisms based on eliminativism about higher-level explanations and sketch a number of empirical conditions that lower-level explanations would have to meet to fully explain higher-level events. (shrink)

This paper analyzes what it means for philosophy of science to be normative. It argues that normativity is a multifaceted phenomenon rather than a general feature that a philosophical theory either has or lacks. It analyzes the normativity of philosophy of science by articulating three ways in which a philosophical theory can be normative. Methodological normativity arises from normative assumptions that philosophers make when they select, interpret, evaluate, and mutually adjust relevant empirical information, on which they base their philosophical theories. (...) Object normativity emerges from the fact that the object of philosophical theorizing can itself be normative, such as when philosophers discuss epistemic norms in science. Metanormativity arises from the kind of claims that a philosophical theory contains, such as normative claims about science as it should be. Distinguishing these three kinds of normativity gives rise to a nuanced and illuminating view of how philosophy of science can be normative. (shrink)

Despite several decades of criticism, dichotomous thinking about behavioral development remains widespread and influential. This is particularly true in study of birdsong development, where it has become increasingly common to diagnose songs, elements of songs, or precursors of songs as either innate or learned on the basis of isolation-rearing experiments. The theory of sensory templates has encouraged both the dichotomous approach and an emphasis on structural rather than functional aspects of song development. As a result, potentially important lines of investigation (...) have been overlooked and the interpretation of existing data is often flawed. Evidence for a genetic origin of behavioraldifferencesis frequently interpreted as evidence for the genetic determination of behavioralcharacters. The technique of isolation rearing remains the methodology of choice for many investigators, despite the fact that it offers only a rather crude analysis of the contribution of experience to song development and provides no information at all about genetic contributions to development. The latter could in principle be elucidated by the application of developmental-genetic techniques, but it is unlikely that these can easily be applied to the study of birdsong. Because developmental questions are so often posed in terms of the learned–innate dichotomy, “experience” is taken to be synonymous with “learning” and the possible role of nonobvious contributions to song development has largely been ignored. An alternative approach, based on Daniel Lehrman's interactionist theory of development, permits a more thorough appreciation of the problems that have yet to be addressed, and provides a more secure conceptual foundation for theories of song development. (shrink)

The inapplicability of variations on theory reduction in the context of genetics and their irrelevance to ongoing research has led to an anti-reductionist consensus in philosophy of biology. One response to this situation is to focus on forms of reductive explanation that better correspond to actual scientific reasoning (e.g. part–whole relations). Working from this perspective, we explore three different aspects (intrinsicality, fundamentality, and temporality) that arise from distinct facets of reductive explanation: composition and causation. Concentrating on these aspects generates new (...) forms of reductive explanation and conditions for their success or failure in biology and other sciences. This analysis is illustrated using the case of protein folding in molecular biology, which demonstrates its applicability and relevance, as well as illuminating the complexity of reductive reasoning in a specific biological context. (shrink)

In his critical notice, Rosenberg (1991) raises three objections to my evolutionary account of science: whether it is more than a week metaphor, the compatibility of my past objections to reduction and my current advocacy of viewing selection in terms of replication and interaction, and finally, the feasibility of identifying appropriate replicators and interactors in biological evolution, let alone conceptual evolution. I discuss each of these objections in turn.

We analyse theories and research approaches in ecology and find that they fall into two internally homogeneous groups of linked ideas, each comprising a unique set of premises. The two sets of interpretive statements are thus mutually exclusive; they constitute alternative theoretical developments in ecology and should not be seen as complementary. They can, therefore, be considered two paradigms (Kuhn, 1962). Our interpretation is supported by the minimal overlap, if any, in the premises and research directions of the two approaches. (...) We label the dominant group of ideas the demographic paradigm and the less developed one the autecological paradigm. The internal logic of the demographic paradigm of ecology is strongly developed and consistent. Its premises and logic extend into current models of population genetics, biogeography, palaeontology, evolutionary theory and conservation biology. Nevertheless, many phenomena contradict the premises of the demographic paradigm; these contradictions cannot be accommodated within its theoretical framework without major disruptions in logic ensuing. Such phenomena can, in contrast, be understood in terms of the autecological paradigm. Because the status and strengths of the autecological paradigm are generally unrecognised and because autecology is frequently misrepresented in the literature, we redefine its premises and clarify its structure and aims as an aid to its future development. (shrink)

The concept of fitness has generated a lot of discussion in philosophy of biology. There is, however, relative agreement about the need to distinguish at least two uses of the term: ecological fitness on the one hand, and population genetics fitness on the other. The goal of this paper is to give an explication of the concept of ecological fitness by providing a reconstruction of the theory of natural selection in which this concept was framed, that is, based on the (...) way the theory was put to use in Darwin’s main texts. I will contend that this reconstruction enables us to account for the current use of the theory of natural selection. The framework presupposed in the analysis will be that of metatheoretical structuralism. This framework will provide both a better understanding of the nature of ecological fitness and a more complete reconstruction of the theory. In particular, it will provide what I think is a better way of understanding how the concept of fitness is applied through heterogeneous cases. One of the major advantages of my way of thinking about natural selection theory is that it would not have the peculiar metatheoretical status that it has in other available views. I will argue that in order to achieve these goals it is necessary to make several concepts explicit, concepts that are frequently omitted in usual reconstructions. (shrink)

Within evolutionary biology a distinction is frequently made between proximate and ultimate causes. One apparently plausible interpretation of this dichotomy is that proximate causes concern processes occurring during the life of an organism while ultimate causes refer to those processes (particularly natural selection) that shaped its genome. But ultimate causes are not sought through historical investigations of an organisms lineage. Rather, explanations referring to ultimate causes typically emerge from functional analyses. But these functional analyses do not identify causes of any (...) kind, much less ultimate ones. So-called ultimate explanations are not about causes in any sense resembling those of proximate explanations. The attitude, implicit in the term ultimate cause, that these functional analyses are somehow superordinate to those involving proximate causes is unfounded. Ultimate causes are neither ultimate nor causes. (shrink)

Definitions of the term gene typically superimpose molecular genetics onto Mendelism. What emerges are persistent attempts to regard the gene as a unit of structure and/or function, language that creates multiple meanings for the term and fails to acknowledge the diversity of gene architecture. I argue that coherence at the molecular level requires abandonment of the classical unit concept and recognition that a gene is constructed from an assemblage of domains. Hence, a domain set (1) conforms more closely to empirical (...) evidence for genetic organization of DNA regions capable of transcription and (2) has ontological properties lacking in the traditional unit definition. (shrink)

This paper is a response to Dickemann’s review ofPedophilia: Biosocial Dimensions. Her main criticism of the book is its inappropriate application of ethology to human sexology and its natural variations. She proposes instead the superiority of the “social constructionist” perspective. The “Phylogenetic Fallacy” of which her review speaks results from her erroneously having attributed ethological arguments about the phylogeny of coordinated motor patterns and sensory releasing stimuli to higher levels of behavioral-ecological strategies to which such arguments were never applied. Because (...) no convincingly adaptive function of human pedophilia could be found at this higher level, as a working hypothesis, variant erotic age and gender orientations were both tentatively conceptualized as by-products of Darwinian natural selection for heterosexual “adultophilia.” The social and political implications of this perspective, when compared to social constructionism, are discussed. (shrink)

Biochemical kinds such as proteins pose interesting problems for philosophers of science, as they can be studied from the points of view of both biology and chemistry. The relationship between the biological functions of biochemical kinds and the microstructures that they are related to is the key question. This leads us to a more general discussion about ontological reductionism, microstructuralism, and multiple realization at the biology-chemistry interface. On the face of it, biochemical kinds seem to pose a challenge for ontological (...) reductionism and hence motivate a dual theory of chemical and biological kinds, a type of pluralism about natural kinds. But it will be argued that the challenge, which is based on multiple realization, can be addressed. The upshot is that there are reasonable prospects for ontological reductionism about biochemical kinds, which corroborates natural kind monism. (shrink)