The main objective of this work is to analyze the intention to reduce some areas of Ecology to Physiology. The origin of this research of reduction was done through consolidation of metabolic ecological theory in first years of XXIst century. Considering this objective, general framework was based on the proposal of Sahotra Sarkar.

Token physicalism is often viewed as a modest and unproblematic physicalist commitment, as contrasted with type physicalism. This paper argues that the prevalence of functional individuation in biology creates serious problems for token physicalism, because the latter requires that biological entities can be individuated physically and without reference to biological functioning. After characterizing the main philosophical roles for token physicalism, I describe the distinctive uses of functional individuation in models of biological processes. I then introduce some requirements on token identity (...) claims that arise from a position on individuation and identity known as sortalism. An examination of biological examples shows that these sortalist requirements cannot be plausibly met due to differences between individuation by functional biological criteria and by physical criteria. Even without assuming sortalism, token physicalism faces the more basic problem of excluding functionally irrelevant detail from the individuation of biological tokens. I close by suggesting that the philosophical roles for token identity are better fulfilled by a notion of token composition, which promotes a hierarchical picture of individuality. (shrink)

Explanations in genetics have intriguing aspects to both biologists and philosophers, and there is no account that satisfactorily elucidates such explanations. The aim of this article is to analyze the kind of explanations usually given in Classical (Transmission) Genetics (CG) and to present in detail the application of an account of explanation as ampliative, specialized nomological embedding to elucidate the such explanations. First, we present explanations in CG in the classical format of inferences with the explanans as the premises and (...) the explanandum as the conclusion and compare them with explanations in other paradigmatic explanatory fields such as Classical Mechanics. Second, we summarize the main aspects discussed in the literature with regard the peculiarities of genetic explanations. Third, we introduce the account of scientific explanation as ampliative, specialized nomological embedding making use of Sneedian structuralism, in particular the notions of theory-net, fundamental law or guiding principle, specialization, and special laws. Finally, we apply this account to the case of CG and show that this analysis sheds light to the intriguing aspects of genetic explanations and remove most of their alleged oddities. (shrink)

Reductionism is a central issue in the philosophy of biology. One common objection to reduction is that molecular explanation requires reference to higher-level properties, which I refer to as the context objection. I respond to this objection by arguing that a well-articulated notion of a mechanism and what I term mechanism extension enables one to accommodate the context-dependence of biological processes within a reductive explanation. The existence of emergent features in the context could be raised as an objection to the (...) possibility of reduction via this strategy. I argue that this objection can be overcome by showing that there is no tenable argument for the existence of emergent properties that are not susceptible to a reductive explanation. (shrink)

Philosophers have proposed various kinds of relations between Mendelian genetics and molecular biology: reduction, replacement, explanatory extension. This paper argues that the two fields are best characterized as investigating different, serially integrated, hereditary mechanisms. The mechanisms operate at different times and contain different working entities. The working entities of the mechanisms of Mendelian heredity are chromosomes, whose movements serve to segregate alleles and independently assort genes in different linkage groups. The working entities of numerous mechanisms of molecular biology are larger (...) and smaller segments of DNA plus related molecules. Discovery of molecular DNA mechanisms filled black boxes that were noted, but unilluminated, by Mendelian genetics. (shrink)

In this paper I present a model of rational belief change, and I show how to use it to obtain a better insight into the debate about the nature of pneumococcal transformation, genes and DNA that took place in the forties, as a result of Oswald T. Avery’s work. The model offers a particular elaboration of the concept of inference to the best explanation, along decision theoretic lines. Within this framework, I distinguish different senses in which Avery’s team can be (...) said to have proceeded with caution, thus throwing some light upon a persistent source of disagreement among researchers in the history of genetics. In addition, I explain why we are entitled to say that rival parties such as physicist Maclyn McCarty and biochemist Alfred Mirsky were epistemically rational, in spite of the fact that they reached different conclusions on the basis of the same evidence. (shrink)

Not all models are explanatory. Some models are data summaries. Some models sketch explanations but leave crucial details unspecified or hidden behind filler terms. Some models are used to conjecture a how-possibly explanation without regard to whether it is a how-actually explanation. I use the Hodgkin and Huxley model of the action potential to illustrate these ways that models can be useful without explaining. I then use the subsequent development of the explanation of the action potential to show what is (...) required of an adequate mechanistic model. Mechanistic models are explanatory. (shrink)

This paper will examine the nature of mechanisms and the distinction between the relevant and irrelevant parts involved in a mechanism’s operation. I first consider Craver’s account of this distinction in his book on the nature of mechanisms, and explain some problems. I then offer a novel account of the distinction that appeals to some resources from Mackie’s theory of causation. I end by explaining how this account enables us to better understand what mechanisms are and their various features.

Some explanations are relatively abstract: they abstract away from the idiosyncratic or messy details of the case in hand. The received wisdom in philosophy is that this is a virtue for any explanation to possess. I argue that the apparent consensus on this point is illusory. When philosophers make this claim, they differ on which of four alternative varieties of abstractness they have in mind. What’s more, for each variety of abstractness there are several alternative reasons to think that the (...) variety of abstractness in question is a virtue. I identify the most promising reasons, and dismiss some others. The paper concludes by relating this discussion to the idea that explanations in biology, psychology and social science cannot be replaced by relatively micro explanations without loss of understanding. (shrink)

Some explanations in social science, psychology and biology belong to a higher level than other explanations. And higher explanations possess the virtue of abstracting away from the details of lower explanations, many philosophers argue. As a result, these higher explanations are irreplaceable. And this suggests that there are genuine higher laws or patterns involving social, psychological and biological states. I show that this ‘abstractness argument’ is really an argument schema, not a single argument. This is because the argument uses the (...) ‘is lower than’ relation, and this relation admits of different readings. I then suggest four rigorous definitions of the ‘is lower than’ relation, and show that the abstractness argument’s prospects are much brighter for some of these definitions than for others. To show this, I evaluate the so-called ‘disjunctive threat’ to the abstractness argument. (shrink)

Contribution to a symposium on Kostas Gavroglu and Ana Simões, Neither Physics nor Chemistry, The MIT Press, Cambridge, Massachusetts.

This paper discusses some philosophical and historical connections between, and within, nineteenth century evolutionism and microscopical research. The principal actors are mainly Darwin, Schleiden, Whewell and the "London Doctors," Arthur Henfrey and Edwin Lankester. I demonstrate that the apparent alliances—particularly Darwin/Schleiden (through evolutionism) and Schleiden/Whewell (through Kantian philosophy of science)—obscure the deep methodological differences between evolutionist and microscopical biology that lingered on until the mid-twentieth century. Through an understanding of the little known significance of Schleiden's programme of microscopical research and (...) by comparing certain features of his methodology to the activities of the "London Doctors," we can identify the origin of this state of affairs. In addition, the outcome provides an insight into a critique of Buchdahl's view on Schleiden's philosophical conception. (shrink)

This paper discusses some philosophical and historical connections between, and within, nineteenth century evolutionism and microscopical research. The principal actors are mainly Darwin, Schleiden, Whewell and the “London Doctors,” Arthur Henfrey and Edwin Lankester. I demonstrate that the apparent alliances—particularly Darwin/Schleiden (through evolutionism) and Schleiden/Whewell (through Kantian philosophy of science)—obscure the deep methodological differences between evolutionist and microscopical biology that lingered on until the mid-twentieth century. Through an understanding of the little known significance of Schleiden’s programme of microscopical research and (...) by comparing certain features of his methodology to the activities of the “London Doctors,” we can identify the origin of this state of affairs. In addition, the outcome provides an insight into a critique of Buchdahl’s view on Schleiden’s philosophical conception. (shrink)

We reconstruct genetic determinism as a reductionist thesis to the effect that the molecular properties of cells can be accounted for to a great extent by their genetic outfit. The non-reductionist arguments offered at this molecular level often use the relationship between structure and function as their point of departure. By contrast, we develop a non-reductionist argument that is confined to the structural characteristics of biomolecules; no appeal to functions is made. We raise two kinds of objections against the reducibility (...) claim underlying genetic determinism. First, some conceptual distinctions at the protein level cannot be captured on a genetic basis. A one-to-many relationship between DNA sequences and proteins emerges from them. Second, the relationship between genes and proteins is characterized by explanatory loops or reciprocal explanatory dependence. The presence of proteins is explained by the transcription from corresponding DNA sequences, and the latter is in turn accounted for by the action of proteins. By contrast, a reductive account requires a unidirectional explanatory dependence. (shrink)

In the grand tradition, philosophical ontology was considered logically and epistemologically prior to scientific ontology. Like many contemporary philosophers of science, we consider this to be a mistake. There is two-way traffic between philosophical and scientific ontologies; the more we learn about what there actually is, the more we learn about what can be and what must be, and vice versa. But that is not the present topic; here we focus on the ontology or ontologies of science, not traditional philosophical (...) ontologies or the traffic between scientific and philosophical ontologies. (shrink)

This paper addresses the political constraints on science through a pragmatist critique of Philip Kitcher’s account of “well-ordered science.” A central part of Kitcher’s account is his analysis of the significance of items of scientific research: contextual and purpose-relative scientific significance replaces mere truth as the aim of inquiry. I raise problems for Kitcher’s account and argue for an alternative, drawing on Peirce’s and Dewey’s theories of problem-solving inquiry. I conclude by suggesting some consequences for understanding the proper conduct of (...) science in a democracy. (shrink)

Despite the ubiquity of “levels of organization” in the scientific literature, a nascent “levels skepticism” now claims that the concept of levels is an inherently flawed, misleading, or otherwise inadequate notion for understanding how life scientists produce knowledge about the natural world. However, levels skeptics rely on the maligned “layer-cake” account of levels stemming from Oppenheim and Putnam’s defense of the unity of science for their critical commentary. Recourse to layer-cake levels is understandable, as it is arguably the default conception (...) of levels in philosophy. However, relying on this conception of levels undermines the initial plausibility of general dismissals of the concept, because the problems skeptics identify within the “basic idea” of the concept “levels” are merely ones already widely acknowledged in this conception. I illustrate this “guilt by association” by looking at the embedded role of “levels” in articulating intertheoretical reductionism during the latter part of the 20th century. I conclude by suggesting a methodological framework focusing on local usage patterns as a promising means for future analysis of the levels concept. (shrink)

The discussion presents a framework of concepts that is intended to account for the rationality of semantic change and variation, suggesting 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 components, and that change in the concept’s inferential role and reference can be accounted for as being rational relative (...) to the third component, the concept’s epistemic goal. This framework is illustrated and defended by application to the history of the gene concept. It is explained how the molecular gene concept grew rationally out of the classical gene concept despite a change in reference, and why the use and reference of the contemporary molecular gene concept may legitimately vary from context to context. (shrink)

Review essay of The Philosophy of Experimental Biology by Marcel Weber (Cambridge University Press, 2005).

This essay analyzes and develops recent views about explanation in biology. Philosophers of biology have parted with the received deductive-nomological model of scientific explanation primarily by attempting to capture actual biological theorizing and practice. This includes an endorsement of different kinds of explanation (e.g., mathematical and causal-mechanistic), a joint study of discovery and explanation, and an abandonment of models of theory reduction in favor of accounts of explanatory reduction. Of particular current interest are philosophical accounts of complex explanations that appeal (...) to different levels of organismal organization and use contributions from different biological disciplines. The essay lays out one model that views explanatory integration across different disciplines as being structured by scientific problems. I emphasize the philosophical need to take the explanatory aims pursued by different groups of scientists into account, as explanatory aims determine whether different explanations are competing or complementary and govern the dynamics of scientific practice, including interdisciplinary research. I distinguish different kinds of pluralism that philosophers have endorsed in the context of explanation in biology, and draw several implications for science education, especially the need to teach science as an interdisciplinary and dynamic practice guided by scientific problems and explanatory aims. (shrink)

The paper works towards an account of explanatory integration in biology, using as a case study explanations of the evolutionary origin of novelties-a problem requiring the integration of several biological fields and approaches. In contrast to the idea that fields studying lower level phenomena are always more fundamental in explanations, I argue that the particular combination of disciplines and theoretical approaches needed to address a complex biological problem and which among them is explanatorily more fundamental varies with the problem pursued. (...) Solving a complex problem need not require theoretical unification or the stable synthesis of different biological fields, as items of knowledge from traditional disciplines can be related solely for the purposes of a specific problem. Apart from the development of genuine interfield theories, successful integration can be effected by smaller epistemic units (concepts, methods, explanations) being linked. Unification or integration is not an aim in itself, but needed for the aim of solving a particular scientific problem, where the problem's nature determines the kind of intellectual integration required. (shrink)

There is a widely shared belief that the higher-level sciences can provide better explanations than lower-level sciences. But there is little agreement about exactly why this is so. It is often suggested that higher-level explanations are better because they omit details. I will argue instead that the preference for higher-level explanations is just a special case of our general preference for informative, logically strong, beliefs. I argue that our preference for informative beliefs entirely accounts for why higher-level explanations are sometimes (...) better—and sometimes worse—than lower-level explanations. The result is a step in the direction of the unity of science hypothesis. 1Introduction2Background: Is Omitting Details an Explanatory Virtue? 2.1Anti-reductionist arguments2.2Reductionist argument2.3Logical strength3Bases, Links and Logical Strength4Functionalism and Fodor’s Argument5Two Generalizations6Should the Base Really Be Maximally Strong?7Anti-reductionist Arguments Regarding the Base8Should the Antecedent of the Link Really Be Maximally Weak? (shrink)

I defend a pragmatist reinterpretation of Sellars’s famous manifest-scientific distinction. I claim that in order to do justice to this important distinction we must first recognize, despite what philosophers—including, arguably, Sellars—often make of it, that the distinction does not draw an epistemological or metaphysical boundary between different kinds of objects and events, but a pragmatic boundary between different ways in which we interact with objects and events. Put differently, I argue that the manifest-scientific distinction, in my view, can be best (...) understood, not as a metaphysical distinction between apparent and real objects and events, or an epistemological distinction between perceptible and imperceptible objects and events, but rather as a distinction, which is not necessarily rigid over time, between distinct ways in which we collectively deal, in practice, with objects and events. (shrink)

Why do we value higher-level scientific explanations if, ultimately, the world is physical? An attractive answer is that physical explanations often cite facts that don’t make a difference to the event in question. I claim that to properly develop this view we need to commit to a type of deterministic chance. And in doing so, we see the theoretical utility of deterministic chance, giving us reason to accept a package of views including deterministic chance.

Shapiro has suggested that the empirical plausibility of the multiple realizability of human-like minds is dubious, because a contrary thesis, the Mental Constraint Thesis, enjoys positive empirical evidence. The Mental Constraint Thesis states that, given the actual physical laws, there is only one way to realize a human-like mind. I will suggest, however, that the Mental Constraint Thesis is not a contrary to the empirical multiple realizability thesis relevant to psychological reduction or autonomy and, as a consequence, has no bearing (...) on those classificatory issues. (shrink)

We present a reconstruction of so-called classical, formal or Mendelian genetics using a notation which we believe is more legible than that of earlier accounts, and lends itself easily to computer implementation, for instance in PROLOG. By drawing from, and emending, earlier work of Balzer and Dawe (1986,1997), the present account presents the three most important lines of development of classical genetics: the so-called Mendel's laws, linkage genetics and gene mapping, in the form of a theory-net. This shows that the (...) set theoretic representation format used in the structuralist approach to the philosophy of science also applies to the domain of genetic theories. There construction is intended to lend more clarity to theme thodological, philosophical and didactical discussions of the foundations of genetics, and on the other hand to defend a formally, logically minded view of theories which seems to have become contested through the work of Feyerabend, Kuhn and Kitcher. (shrink)

Kenneth Waters and Marcel Weber argue that the joint use of distinct gene concepts and the transfer of knowledge between classical and molecular analyses in contemporary scientific practice is possible because classical and molecular concepts of the gene refer to overlapping chromosomal segments and the DNA sequences associated with these segments. However, while pointing in the direction of coreference, both authors also agree that there is a considerable divergence between the actual sequences that count as genes in classical genetics and (...) molecular biology. The thesis advanced in this paper is that the referents of classical and molecular gene concepts are coextensive to a higher degree than admitted by Waters and Weber, and therefore coreference can provide a satisfactory account of the high level of integration between classical genetics and molecular biology. In particular, I argue that the functional units/cistrons identified by classical techniques overlap with functional elements entering the composition of molecular transcription units, and that the precision of this overlap can be improved by conducting further experimentation. (shrink)

This paper explores the relationships that various applied ethics bear to each other, both in particular disciplines and more generally. The introductory section lays out the challenge of coming up with such an account and, drawing a parallel with the philosophy of science, offers that applied ethics may either be unified or disunified. The second section develops one simple account through which applied ethics are unified, vis-à-vis ethical theory. However, this is not taken to be a satisfying answer, for reasons (...) explained. In the third section, specific applied ethics are explored: biomedical ethics; business ethics; environmental ethics; and neuroethics. These are chosen not to be comprehensive, but rather for their traditions or other illustrative purposes. The final section draws together the results of the preceding analysis and defends a disunity conception of applied ethics. (shrink)

There is a familiar tension between the two main components of non-reductive physicalism, which are physicalism, on the one hand, and the non-reducibility or autonomy of so-called special sciences (i.e., sciences other than physics), on the other. While it is often claimed that this tension can be satisfactorily resolved by adopting the subset account of realization (defended by e.g., Shoemaker (2001) and Wilson (2011)), this paper challenges that popular view, by elaborating some critical comments by Funkhouser (2014). Then, after examining (...) Funkhouser’s own position, this paper proposes a new way of resolving the aforementioned tension, which consists in refining the subset account’s analysis of realization on the basis of various dependence relations between causal powers. (shrink)

Abstract: There has recently been controversy over the existence of 'multiple realization' in addition to some confusion between different conceptions of its nature. To resolve these problems, we focus on concrete examples from the sciences to provide precise accounts of the scientific concepts of 'realization' and 'multiple realization' that have played key roles in recent debates in the philosophy of science and philosophy of psychology. We illustrate the advantages of our view over a prominent rival account ( Shapiro, 2000 and (...) 2004 ) and use our work to rebut recent objections to the long-standing claim that psychological properties are multiply realized. For we use scientific evidence, in combination with our more precise theoretical framework, to show that we have strong reason to believe that psychological properties are indeed multiply realized both at the biochemical and neuronal levels. (shrink)

A substantial guide providing an overview of both physicalism and metaphysical naturalism, reviewing both questions of formulation and justification for both doctrines. Includes a diagnostic strategy for understanding talk of naturalism as a metaphysical thesis.

Scientifically speaking, quantum mechanics (QM) is the most successful theory ever made. Philosophically speaking, however, it is the most controversial theory. Its basic principles seem to contravene our deepest intuitions about reality, which are reflected in the metaphysical commitments of classical mechanics (CM). The aim of this paper is twofold. First, I argue that QM implies an ontological challenge, and not merely an “ontic” one, as it has been traditionally interpreted in the analytic tradition. Second, I suggest that positions known (...) as “ontological pluralism” exhibit an internal weakness due to its unwarranted compromise to a representational view of scientific theories. (shrink)

This paper argues against the view that the standard explanation of phase transitions in statistical mechanics may be considered a causal explanation, a distortion that can nevertheless successfully represent causal relations.

What is a gene? Does it represent a natural kind, or is it just a tool for genomics? A clear answer to these questions has been challenged by postgenomic discoveries. In response, I will argue that the gene can be deemed a natural kind as it satisfies some requirements for genuine kindhood. Specifically, natural kinds are projectible categories in our best scientific theories, and they represent nodes in the causal network of the world (as in Khalidi. Natural Categories and Human (...) Kinds: Classification in the Natural and Social Sciences. Cambridge University Press, Cambridge, 2013; Khalidi. Synthese 195: 1379–1396, 2018; Khalidi. Are Sexes Natural Kinds, In: Dasgupta S, Weslake B (eds) Current Controversies in Philoso-phy of Science. Routledge, New York, 2020; Khalidi. Philos Sci 88:1–21, 2021). In Sect. 2, I will present a brief history of the gene and the controversy over its status. In Sect. 3, I will introduce the account of natural kinds considered in this paper. In Sect. 4, I will first present the relevant definition of genes and how they can be classified. Then, I will argue that the gene can be considered a natural kind as it satisfies the criteria for natural kindhood. Section 5 concludes. (shrink)

Scientific revolution has been one of the most controversial topics in the history and philosophy of science. Yet it has been no consensus on what is the best unit of analysis in the historiography of scientific revolutions. Nor is there a consensus on what best explains the nature of scientific revolutions. This chapter provides a critical examination of the historiography of scientific revolutions. It begins with a brief introduction to the historical development of the concept of scientific revolution, followed by (...) an overview of the five main philosophical accounts of scientific revolutions. It then challenges two historiographical assumptions of the philosophical analyses of scientific revolutions. (shrink)

Philip Kitcher has advocated and advanced an influential antireductionist picture of science on which the higher-level sciences pursue their aims largely independently of the lower-level sciences -- a view of the sciences as autonomous. Explanatory autonomy as Kitcher understands it is incompatible with explanatory reductionism, the view that a high-level explanation is inevitably improved by providing a lower-level explanation of its parts. This paper explores an alternative conception of autonomy based on another major theme of Kitcher's philosophy of science: the (...) importance of the division of cognitive labor. That the sciences are in practice autonomous is compatible with reductionism, I argue, if we understand the high-level sciences' systematic explanatory disregard of lower-level details of implementation as practically, rather than intellectually, motivated. (shrink)

This volume argues for a new image of science that understands both natural and social phenomena to be the product of mechanisms, casting the work of science as an effort to understand those mechanisms. Glennan offers an account of the nature of mechanisms and of the models used to represent them in physical, life, and social sciences.

Convincing disputes about explanatory reductionism in the philosophy of biology require a clear and precise understanding of what a reductive explanation in biology is. The central aim of this book is to provide such an account by revealing the features that determine the reductive character of a biological explanation. Chapters I-IV provide the ground, on which I can then, in Chapter V, develop my own account of explanatory reduction in biology: Chapter I reveals the meta-philosophical assumptions that underlie my analysis (...) of reduction, Chapter II introduces the previous debate about reduction in the philosophy of biology by pointing out the most crucial lessons one should learn from this debate, Chapter III critically discusses the two perspectives on explanatory reduction that have been proposed in the philosophy of biology so far, and Chapter IV clarifies in what ways the issue of reduction is entangled with the issue of explanation. In Chapter V I present my own account of explanatory reduction. My main claim is that reductive explanations in the biological sciences possess three main characteristics: they explain the behavior of a biological system S, first, exclusively in terms of factors that are located on a lower level of organization than S, second, by focusing on factors that are internal to S , and third, by describing the genuine parts of S only as “parts in isolation”. This account is ontic because it traces the reductivity of an explanation back to certain relations that exist in the world. (shrink)

A long-standing problem in understanding goal-directed systems has been the insufficiency of mechanistic explanations to make sense of them. This paper offers a solution to this problem. It begins by observing the limitations of mechanistic decompositions when it comes to understanding physical fields. We argue that introducing the field concept, as it has been developed in field theory, alongside mechanisms is able to provide an account of goal directedness in the sciences.