Reduction in Biology

This article defends the notion of downward causation, relating it to a notion of conditional independence.

The historical development of debates about reduction testifies to us that reductionism in biology must proceed by providing a precise and complete causal explanation for every biological phenomenon at the level of molecules. An intertheoretical reduction model was proposed in biology but proved unsuccessful due to its inability to accommodate and explain the success of molecular biology. Ever since the molecular structure of the gene was discovered, actual biological research has successfully generated explanations for complex biological facts in terms of (...) the predicates of molecular biology. Biological phenomena, which classical functional biology explains only with limited powers, are more accurately described and comprehensively explained as the reduction processes advance with molecular biology. It is clear that the reductionist research program of molecular biology is the best account of success and progress in biology. (shrink)

In this work I propose a theory of evolution as a process of unfolding. This theory is based on four logically concatenated principles. The principle of evolutionary order establishes that the more complex cannot be generated from the simpler. The principle of origin establishes that there must be a maximum complexity that originates the others by logical deduction. Finally, the principle of unfolding and the principle of actualization guarantee the development of the evolutionary process from the simplest to the most (...) complex. These logical principles determine the existence of a virtual ideological matrix that contains the sequence of the preformed and folded morphogenetic fields. In this manner, the evolutionary process consists of the sequential unfolding and actualization of these fields, which is motorized by a process of teleologization carried out by the opening consciousness of the forms included in the fields of the ideological matrix. This theory leads to a radical change of perspective regarding the materialist worldview, and places life at the center of the evolutionary process as an activity carried out by a consciousness that seeks to fulfill a purpose by actualizing its own potentialities. (shrink)

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)

Philosophers have traditionally addressed the issue of scientific unification in terms of theoretical reduction. Reductive models, however, cannot explain the occurrence of unification in areas of science where successful reductions are hard to find. The goal of this essay is to analyse a concrete example of integration in biology—the developmental synthesis—and to generalize it into a model of scientific unification, according to which two fields are in the process of being unified when they become explanatorily relevant to each other. I (...) conclude by suggesting that this methodological conception of unity, which is independent of the debate on the metaphysical foundations of science, is closely connected to the notion of interdisciplinarity. 1 Introduction2 Some Troubles with Theory Reduction3 Interfield and Mechanistic Unification4 Foundations of the Developmental Synthesis5 Explanatory Relevance6 Concluding Remarks. (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)

Reference to mechanisms is virtually ubiquitous in science and its philosophy. Yet, the concept of a mechanism remains largely unanalyzed; So too for its possible applications in thinking about scientific explanation, experimental practice, and theory structure. This dissertation investigates these issues in the context of contemporary neurobiology. ;The theories of neurobiology are hierarchically organized descriptions of mechanisms that explain functions. Mechanisms are the coordinated activities of entities by virtue of which that function is performed. Since the activities composing mechanisms are (...) often susceptible to mechanical redescription themselves, theories in neurobiology have a characteristic hierarchical structure. The activities of entities at one level are the sub-activities of those at a higher level. ;This hierarchy reveals a fundamental symmetry of functional and mechanical descriptions. Functions are privileged activities of entities; they are privileged because they constitute a stage in some higher-level mechanism. The privileged activities of entities, in turn, are explained by detailing the stages of activity in the lower-level mechanism. Functional and mechanical descriptions are different tools for situating activities, properties, and entities into a hierarchy of activities. They are not competing kinds of description. Experimental techniques for testing such descriptions reflect this symmetry. ;Philosophical discussions of inter-level explanatory relationships have traditionally been framed by reference to inter-theoretic reduction models. The representational strictures of first order predicate calculus and the epistemological strictures logical empiricism combine in this reduction model to focus attention upon issues of identity and deriveability; these are entirely peripheral to the explanatory aims of mechanical explanation. Mechanical explanation is causal. Derivational models of explanation do not adequately reflect the importance of activities in rendering phenomena intelligible. ;Activities are kinds of change. "Bonding," "diffusing," "transcribing," "opening," and "attracting" all describe different kinds of transformation. Salmon's modified process theory is helpful in understanding the role of entities and properties in causal interactions; but it ultimately makes no room for kinds of change in the explanatory cupboard. We make change intelligible by identifying and characterizing its different kinds and relating these to activities that are taken to be fundamental for a science at a time. (shrink)

The impact of Niels Bohr’s 1932 “Light and Life” lecture on Max Delbrück’s lifelong search for a form of “complementarity” in biology is well documented and much discussed, but the precise nature of that influence remains subject to misunderstanding. The standard reading, which sees Delbrück’s transition from physics into biology as inspired by the hope that investigation of biological phenomena might lead to a breakthrough discovery of new laws of physics, is colored much more by Erwin Schrödinger’s What Is Life? (...) than is often acknowledged. Bohr’s view was that teleological and mechanistic descriptions are mutually exclusive yet jointly necessary for an exhaustive understanding of life. Although Delbrück’s approach was empirical and less self‐consciously philosophical, he shared Bohr’s hope that scientific investigation would vindicate the view that at least some aspects of life are not reducible to physico‐chemical terms. (shrink)

Reductionism and antireductionism are among the most largely and hotly debated topics in philosophy of biology today. In this section of the volume, aiming to convey the current situation in the philosophy of the natural and life sciences, these topics are specifically addressed in Mehmet Elgin’s paper, focusing on biochemistry. Elgin strongly supports reductionism, first by claiming that the now classical argument based on multiple realizability does not entail anti-reductionism and secondly highlighting how the version of methodological reductionism that biochemistry (...) has been adopting – centered on “the principle that biological functions of biomolecules in living cells can be understood in terms of chemical and physical properties of those molecules”1 – has proved largely successful, teaching “us new knowledge about the biological systems”. Taken together, these two arguments are deemed to provide good grounds for a thorough defence of reductionism. While Elgin chooses biochemistry as his privileged standpoint on the issue, I shall dwell on the stances emerging in the health sciences. Although the health sciences are closely intertwined with – amongst others – biology and biochemistry, they also have their own peculiar features. Referring to some examples taken from different medical disciplines, I will question whether reductionism can be regarded as not only a viable, option, but as the best solution to gain new knowledge about biomedical systems. I shall suggest that considerations arising from current medical research and practice support a pluralistic approach to the topic, in which both reductionist and antireductionist stances can be accommodated in different ways. (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)

The study of mental illness by the methods of molecular genetics is still in its infancy, but the use of genetic markers in psychiatry may potentially lead to a Virchowian revolution in the conception of mental illness. Genetic markers may define novel clusters of patients having diverse clinical presentations but sharing a common genetic and mechanistic basis. Such clusters may differ radically from the conventional classification schemes of psychiatric illness. However, the reduction of even relatively simple Mendelian phenomena to molecular (...) genetics has been shown to be a surprisingly complex and problematic enterprise. Mental illnesses exist at many levels of including social, environmental, and developmental interactions. Reductionistic shifts in the classification of such a disease entity will have to address the interlevel dynamics that take place within the structure of theories of mental illness. The question of how molecular analysis of psychiatric disease will impact on the structure of existing theories and classification systems is the central topic of this paper. (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.

Recently philosophers of biology have argued over whether or not Newtonian mechanics provides a useful analogy for thinking about evolutionary theory. For philosophers, the canonical presentation of this analogy is Sober's. Matthen and Ariew and Walsh, Lewins, and Ariew argue that this analogy is deeply wrong-headed. Here I argue that the analogy is indeed useful, however, not in the way it is usually interpreted. The Newtonian analogy depends on having the proper analogue of Newton's First Law. That analogue is what (...) McShea and Brandon call the Zero Force Evolutionary Law. According to the ZFEL, change, not stasis, is the default state of evolutionary systems. (shrink)

This essay examines the claim “path dependence entails irreversibility” from the point of view of evolutionary biology. I argue that evolutionary irreversibility possesses many faces, sometimes conflicting with path dependence. I propose an account of path dependence that does not rely on irreversibility and explains why it more naturally coexists with the notion of (contingent) irreversibility developed by the Belgian paleontologist Louis Dollo. However, I argue that we should not conceive of this relationship as necessary.

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)

In the context of mechanistic explanation, reductionistic research pursues a decomposition of complex systems into their component parts and operations. Using research on the mechanisms responsible for circadian rhythms, I consider both the gains that have been made by discovering genes and proteins that figure in these intracellular oscillators and also highlight the increasingly recognized need to understand higher-level integration, both between cells in the central oscillator and between the central and peripheral oscillators. This history illustrates a common need to (...) complement reductionistic inquiry with investigations at higher-levels. Unlike most other accounts of reduction, the mechanistic framework accommodates this complementary relationship between reductionistic and systems approaches. (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)