Reduction in Biology

The problem with reductionism in biology is not the reduction, but the implicit attitude of determinism that usually accompanies it. Methodological reductionism is supported by deterministic beliefs, but making such a connection is problematic when it is based on an idea of determinism as fixed predictability. Conflating determinism with predictability gives rise to inaccurate models that overlook the dynamic complexity of our world, as well as ignore our epistemic limitations when we try to model it. Furthermore, the assumption of a (...) strictly deterministic framework is unnecessarily hindering to biology. By removing the dogma of determinism, biological methods, including reductive methods, can be expanded to include stochastic models and probabilistic interpretations. Thus, the dogma of reductionism can be saved once its ties with determinism are severed. In this paper, I analyze two problems that have faced molecular biology for the last 50 years—protein folding and cancer. Both cases demonstrate the long influence of reductionism and determinism on molecular biology, as well as how abandoning determinism has opened the door to more probabilistic and unconstrained reductive methods in biology. (shrink)

The biochemical study of the simplest living systems does not yield the mechanistic results promised by those who deny that life is an irreducible parameter. We show through the complex mechanisms concerned with the replication, repair, and defense of DNA that organisms are organized to maintain their integrity. Mutations and evolution are not always random effects of environmental causes, for the organism is to some extent able to control chance.

Life poses a threat to materialism. To understand the phenomena of animate nature, we make use of a teleological form of explanation that is peculiar to biology, of explanations in terms of what I call the ‘vital categories’ – and this holds even for accounts of underlying physico-chemical ‘mechanisms’. The materialist claims that this teleological form of explanation does not capture what is metaphysically fundamental, whereas her preferred physical form of explanation does. In this essay, I do three things. (1) (...) I argue that the ‘vital categories’, such as life form and life-process, do not reduce to the ‘physical categories’ and show that there are no grounds for the materialist's metaphysically limiting claim; (2) I sketch a positive view on how vital and physical explanations can both apply to a given phenomenon, and on how they interrelate; and (3) I show that this view meshes nicely with evolutionary theory, despite being committed to a form of ‘biological essentialism’. (shrink)

_Conservative Reductionism_ sets out a new theory of the relationship between physics and the special sciences within the framework of functionalism. It argues that it is wrong-headed to conceive an opposition between functional and physical properties and to build an anti-reductionist argument on multiple realization. By contrast, all properties that there are in the world, including the physical ones, are functional properties in the sense of being causal properties, and all true descriptions that the special sciences propose can in principle (...) be reduced to physical descriptions by means of functional reduction, despite multiple realization. The book develops arguments for from the metaphysics of properties and the philosophy of physics. These arguments lead to a conservative ontological reductionism. It then develops functional reduction into a fully-fledged, conservative theory reduction by means of introducing functional sub-types that are coextensive with physical types, illustrating that conservative reductionism by means of case studies from biology. (shrink)

The idea of levels of organization plays a central role in the philosophy of the life sciences. In this article, I first examine the explanatory goals that have motivated accounts of levels of organization. I then show that the most state-of-the-art and scientifically plausible account of levels of organization, the account of levels of mechanism proposed by Bechtel and Craver, is fundamentally problematic. Finally, I argue that the explanatory goals can be reached by adopting a deflationary approach, where levels of (...) organization give way to more well-defined and fundamental notions, such as scale and composition. (shrink)

This introduction to the special section on integration in biology provides an overview of the different contributions. In addition to motivating the philosophical significance of analyzing integration and interdisciplinary research, I lay out common themes and novel insights found among the special section contributions, and indicate how they exhibit current trends in the philosophical study of integration. One upshot of the contributed papers is that there are different aspects to and kinds of integration, so that rather than attempting to offer (...) a universal construal of what integrations is, philosophers have to analyze in concrete cases in what respects particular aspects of scientific theorizing and/or practice are ‘integrative’ and how this instance of integration works and was achieved. (shrink)

Exact sciences are described as sciences whose theories are formalized. These are contrasted to inexact sciences, whose theories are not formalized. Formalization is described as a broader category than mathematization, involving any form/content distinction allowing forms, e.g., as represented in theoretical models, to be studied independently of the empirical content of a subject-matter domain. Exactness is a practice depending on the use of theories to control subject-matter domains and to align theoretical with empirical models and not merely a state of (...) a science. Inexact biological sciences tolerate a degree of “mismatch” between theoretical and empirical models and concepts. Three illustrations from biological sciences are discussed in which formalization is achieved by various means: Mendelism, Weismannism, and Darwinism. Frege’s idea of a “conceptual notation” is used to further characterize the notion of a form/content distinction. (shrink)

I will use the history of phage to focus on the issue of biological explanations; on the relationship between biology and physics; and on the historical problem of the disciplinary autonomy of biology, versus its reduction, which ultimately seeks to place it within the domain of the physical sciences. Paradoxically, the two physicists I focus on most, Neils Bohr and Max Delbrück, represent attempts to preserve the autonomy of biology, each in a very complex way. Once again the problematique here (...) is the nature of biological systems as goal-oriented historical phenomena, that is, as teleological explanations rather than mechanistic accounts of life. (shrink)

The general aim of this paper is to propose a reductionist strategy to higher-level property types. Starting from a common ground in the philosophy of science, I shall elaborate on possible realizer differences of higher-level property types. Because of the realizer types' causal heterogeneity, an introduction of functional sub-types of higher-level properties will be suggested. Each higher-level functional sub-type corresponds to one realizer type. This means that there is the theoretical possibility to reach some kind of type-identity and this opens (...) up the way for theory reduction in a more complete manner. This kind of type-identity will go beyond the common ground of the identity of tokens and their reductive explanation. In the second part of the paper, this reductionist strategy will be applied to a specific debate in the philosophy of biology — the reductionist approach to classical genetics from a molecular point of view. (shrink)

There is the general philosophical question concerning the relationship between physics, which is often taken to be our fundamental and all-encompassing science, on one hand and the special sciences, such as biology and psychology, each of which deals with phenomena in some specially restricted domain, on the other. This paper deals with a narrower question: Are there laws in the special sciences, laws like those we find, or expect to find, in basic physics? Three arguments that are intended to show (...) that there are no such laws are presented and examined. The paper ends with brief remarks concerning the implications of these arguments for explanation and causation in the special sciences. (shrink)

The holism/reductionism debate in evolutionary biology has often been analysed as involving two main phenomenological levels within neo-Darwinism: genetic and organismic. This analytical framework assumes that explanation in evolution is either found in the field of genetics or the field of organismic biology. It is argued here that this framework is far too restrictive to incorporate what at least some founding members of neo-Darwinism had in mind in their search for the ultimate cause of evolution. Dobzhansky's "super-holism" locates this drive (...) in the highest possible entity imaginable — an ontologically unified evolutionary cosmos — while Rensch's ontological "super-reductionism," on the other hand, places it at the lowest possible entity of microphysics, that is, at the level of an energetic field of protopsychical nature. Not only it is suggested that a much-expanded framework is required for analysing the holism/reductionism debate in neo-Darwinism, but also that this new framework may have implications for the conceptualization of the neo-Darwinian movement itself. (shrink)

In the present paper, I shall argue that quantum theory can contribute to reconciling evolutionary biology with the creation hypothesis. After giving a careful definition of the theological problem, I will, in a first step, formulate necessary conditions for the compatibility of evolutionary theory and the creation hypothesis. In a second step, I will show how quantum theory can contribute to fulfilling these conditions. More precisely, I claim that (1) quantum probabilities are best understood in terms of ontological indeterminism, but (...) (2) reflect nevertheless causal openness rather than divine indifference or arbitrariness, and (3) such a genuinely creative universe can be considered as the work of a loving Creator. I ask subsequently whether these necessary conditions are also sufficient for the compatibility of evolutionary theory and the creation hypothesis. Finally, I will show that relating evolutionary biology with theology via quantum theory could also shed some light on the nature of life. (shrink)

To enhance the treatment of relations in biomedical ontologies we advance a methodology for providing consistent and unambiguous formal definitions of the relational expressions used in such ontologies in a way designed to assist developers and users in avoiding errors in coding and annotation. The resulting Relation Ontology can promote interoperability of ontologies and support new types of automated reasoning about the spatial and temporal dimensions of biological and medical phenomena.

During the past few decades, philosophers of biology have debated the issue of reductionism versus anti-reductionism, with both sides often claiming a ‘pluralist’ position. However, both sides also tend to focus on a single research paradigm, which analyzes living things in terms of certain macromolecular components. I offer a case study where biologists pursue other analytic pathways, in a tradition of quantitative genetics that originates with the initially purely mathematical theories of R. A. Fisher, J. B. S. Haldane, and Sewall (...) Wright in the 1930s. Aster Models offers a class of statistical models designed for studying the fitness of plant and animal populations, by integrating the measurements of separate, sequential, non-normally distributed fitness components in novel ways. Their work generates important theoretical and practical results that do not require elaboration by molecular biology, and thus serves as a counterexample to the claims of philosophers whose ‘pluralism’ still harbors reductionist assumptions. (shrink)

Diffusion theory explains in physical terms how materials move through a medium, e.g. water or a biological fluid. There are strong and widely acknowledged grounds for doubting the applicability of this theory in biology, although it continues to be accepted almost uncritically and taught as a basis of both biology and medicine. Our principal aim is to explore how this situation arose and has been allowed to continue seemingly unchallenged for more than 150 years. The main shortcomings of diffusion theory (...) will be briefly reviewed to show that the entrenchment of this theory in the corpus of biological knowledge needs to be explained, especially as there are equally valid historical grounds for presuming that bulk fluid movement powered by the energy of cell metabolism plays a prominent note in the transport of molecules in the living body. First, the theory's evolution, notably from its origins in connection with the mechanistic materialist philosophy of mid nineteenth century physiology, is discussed. Following this, the entrenchment of the theory in twentieth century biology is analyzed in relation to three situations: the mechanism of oxygen transport between air and mammalian tissues; the structure and function of cell membranes; and the nature of the intermediary metabolism, with its implicit presumptions about the intracellular organization and the movement of molecules within it. In our final section, we consider several historically based alternatives to diffusion theory, all of which have their precursors in nineteenth and twentieth century philosophy of science. (shrink)

The timeliness of the problem of reduction is due above all to the successes of application of the techniques of the exact sciences in biology. To the extent that molecular biology "gets down to" the initial, fundamental mechanisms of the processes of life, it is impossible for it to remain purely in the realm of statement of facts; it cannot but affect methodological principles of the study of life. "The history of biology clearly demonstrates the striking regularity with which the (...) problem of reductionism arises each time biological knowledge advances to a new level." The counterposing of mechanism and vitalism, elementarism and organicism, etc., was replaced by new forms of methodological discussion born of the achievements of experimental knowledge of life and the demands that this be formulated into theory. To separate the principle of reduction, productive in current biological research, from biological reductionism based on the elevation of this principle to an absolute is the meaning of the current struggle against mechanistic trends in biology. The mechanicism of the present day rests primarily on the productiveness of the methods of physical chemistry in adding to knowledge of life; and therefore when people speak of the problem of reductionism, discussion of the potentials of the investigation of life by molecular biology and the limits of those potentials takes pride of place. (shrink)

Reductionism in biology concerns the relations between biology and physico-chemic sciences. It is both historically and epistemologically analysed. Two historical moments are studied: the origins of the cell theory and the contact between cell theory and mendellian genetic. Epistemological analysis concerns first the peculiarity of functional explanation. Logical analysis is complemented by a tentative reduction of the function of hemoglobin to his biochemical structure. Second, reduction between theories will be analysed. Finally, the convergence between historical and epistemological analysis will be (...) emphasized. (shrink)

For several decades, economists have been preoccupied with an attempt to place their entire subject on the ‘sound microfoundations’ of general equilibrium theory, with its individualistic premises. However, this project has run into seemingly intractable problems. This essay examines underlying questions such as the appropriate building block of analysis and the structure of explanation in economics. The examination of biology is found to be instructive, due to debates concerning the limitations of reductionism within that discipline. The final part of the (...) paper argues for the autonomy of a non‐reductionist macroeconomics, based on the institution as the unit of analysis. (shrink)

In Molecular Models: Philosophical Papers on Molecular Biology, Sahotra Sarkar presents a historical and philosophical analysis of four important themes in philosophy of science that have been influenced by discoveries in molecular biology. These are: reduction, function, information and directed mutation. I argue that there is an important difference between the cases of function and information and the more complex case of scientific reduction. In the former cases it makes sense to taxonomise important variations in scientific and philosophical usage of (...) the terms function and information . However, the variety of usage of reduction across scientific disciplines (and across philosophy of science) makes such taxonomy inappropriate. Sarkar presents reduction as a set of facts about the world that science has discovered, but the facts in question are remarkably disparate; variously semantic, epistemic and ontological. I argue that the more natural conclusion of Sarkar’s analysis is eliminativism about reduction as a scientific concept. (shrink)

In this work we study the behavior of a time discrete multiregional stochastic model for a population structured in age classes and spread out in different spatial patches between which individuals can migrate. The dynamics of the population is controlled both by reproduction-survival and by migration. These processes take place at different time scales in the sense of the latter being much faster than the former. We incorporate the effect of demographic stochasticity into the population, which results in both dynamics (...) being modelled by multitype Bienaymé–Galton–Watson branching processes. We present a multitype global model that incorporates the effect of both processes and, making use of the existence of different time scales for demography and migration, build a reduced model in which the variables correspond to the total population in each age class. We extend previous results that relate the behavior of the original and the reduced model showing that, given a large enough separation of time scales between demography and migration, we can obtain information about the behavior of the multitype global model through the study of the simpler reduced model. We concentrate on the case where the two systems are supercritical and therefore the expected number of individuals grows to infinity, and show that we can approximate the asymptotic structure of the population vector and the asymptotic population size of the original system through the study of the reduced model. (shrink)

In Making Sense of Life , Keller emphasizes several differences between biology and physics. Her analysis focuses on significant ways in which modelling practices in some areas of biology, especially developmental biology, differ from those of the physical sciences. She suggests that natural models and modelling by homology play a central role in the former but not the latter. In this paper, I focus instead on those practices that are importantly similar, from the point of view of epistemology and cognitive (...) science. I argue that concrete and abstract models are significant in both disciplines, that there are shared selection criteria for models in physics and biology, e.g. familiarity, and that modelling often occurs in a similar fashion. (shrink)

The focus of much recent debate between realists and eliminativists about the propositional attitudes obscures the fact that a spectrum of positions lies between these celebrated extremes. Appealing to an influential theoretical development in cognitive neurobiology, I argue that there is reason to expect such an “intermediate” outcome. The ontology that emerges is a revisionary physicalism. The argument draws lessons about revisionistic reductions from an important historical example, the reduction of equilibrium thermodynamics to statistical mechanics, and applies them to the (...) relationship developing between propositional attitude psychology and this potential neuroscientific successor. It predicts enough conceptual change to rule out a straightforward realism about the attitudes; but at the same time it also resists the eliminativist's comparison of the fate awaiting the propositional attitudes to that befalling caloric fluid, phlogiston, and the like. (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)

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)

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)

Most discussion of the unity of science has concerned what might be called vertical relations between theories: the reducibility of biology to chemistry, or chemistry to physics, and so on. In this paper I shall be concerned rather with horizontal relations, that is to say, with theories of different kinds that deal with objects at the same structural level. Whereas the former, vertical, conception of unity through reduction has come under a good deal of criticism recently (see, e.g., Dupré 1993), (...) horizontal unity has generally been conceded to be an important goal. The most pressing questions about horizontal unification arise in the study of human behavior. Numerous sciences including psychology, economics, anthropology, sociology, and parts of biology, attempt to provide explanations of human behavior. It is possible that some of these sciences may be able to coexist peacefully or even cooperatively. However things do not always go so smoothly, and at least two approaches to human behavior, those deriving from economics and evolutionary biology, often involve clearly imperialist tendencies. Devotees of these approaches are inclined to claim that they are in possession not just of one useful perspective on human behavior, but of the key that will open doors to the understanding of ever wider areas of human behavior. In this paper I shall consider some areas in which economic and evolutionary imperialists are currently staking claims. It is of particular interest to look at situations where two the two imperialist programs are staking the same claim, but limitations of space force me to focus here mainly on economics, and my remarks on evolutionary imperialism will be cursory. As well as some specific insights into the particular strategies of these scientific programs, I hope that my discussion will throw some more general light on the limits of such general theoretical strategies and, thereby, I shall suggest some motivations for adhering to a horizontal pluralism of science that matches the vertical pluralism advocated by anti-reductionists. (shrink)

According to the situation of recent biology it seems to be necessary to continue the theoretical foundation of this science, and especially a foundation beyond physics and metaphysics. The preconditions of such a project are given with the problems of causality, natural law and induction. The discussion of these subjects in modern philosophy of science did not bring useful results, for philosophy of science itself is orientated by physics. On the other hand even the history of these problems in biology (...) shows that the acceptance of physical or philosophical viewpoints leads to invincible difficulties.Therefore, in this paper, I have tried to demonstrate the necessity of analyzing these basic problems in a new way. The conditions and circumstances of a biological phenomenon have a special kind of multidimensional relationship, so that they cannot be reduced to simple linear systems of cause and effect. The fact that biological systems have a lot of retroactive effects makes the description of their causality much more complicated than it is in physics. (shrink)

This collection of revised and new essays argues that biology is an autonomous science rather than a branch of the physical sciences. Ernst Mayr, widely considered the most eminent evolutionary biologist of the 20th century, offers insights on the history of evolutionary thought, critiques the conditions of philosophy to the science of biology, and comments on several of the major developments in evolutionary theory. Notably, Mayr explains that Darwin's theory of evolution is actually five separate theories, each with its own (...) history, trajectory and impact. Ernst Mayr, commonly referred to as the "Darwin of the 20th century" and listed as one of the top 100 scientists of all-time, is Professor Emeritus at Harvard University. What Makes Biology Unique is the 25th book he has written during his long and prolific career. His recent books include This is Biology: The Science of the Living World (Belknap Press, 1997) and What Evolution Is (Basic Books, 2002). (shrink)