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W2805551057 abstract "PHYSIOLOGY’S IMPACTDissecting the Meanings of “Physiology” to Assess the Vitality of the DisciplineMaël Lemoine and Thomas PradeuMaël LemoineImmunoConcept, UMR5164, CNRS & University of Bordeaux, Bordeaux, France* and Thomas PradeuImmunoConcept, UMR5164, CNRS & University of Bordeaux, Bordeaux, France*Published Online:06 Jun 2018https://doi.org/10.1152/physiol.00015.2018MoreSectionsPDF (251 KB)Download PDF ToolsExport citationAdd to favoritesGet permissionsTrack citations ShareShare onFacebookTwitterLinkedInWeChat IntroductionPhysiology is one of the central disciplines on which all biological and medical sciences were historically built (63). However, questions have recently been raised concerning the relevance and vitality of physiology and its ability to make a useful contribution to biological and medical sciences. Physiology is sometimes seen as a discipline of the past that is “dying” in the era of molecular biology and high-throughput DNA sequencing (5, 50, 77, 96). However, close scrutiny would suggest a less clear-cut picture. Not everyone would agree with claims that the intellectual discipline of physiology is dying, or perhaps even already dead (97). They feel that physiology has gradually “disintegrated” precisely because it has given rise to a series of daughter disciplines, such as neurosciences, immunology, and endocrinology (45, 74, 84). According to this view, physiology is not so much “dead” as a key element underlying some of the most dynamic fields in the biological sciences of today, including the various -omics disciplines (120). Some would even defend the view that physiology remains a key field in modern-day biology and that it could perhaps inspire renewal in other biological disciplines, including molecular biology and evolution (24, 51, 84, 86).This conceptual review aims to introduce physiologists to the philosophy of biology and medicine. We argue here that the claims made about the vitality and utility of physiology depend heavily on the definition of “physiology” adopted. We distinguish between two families of definitions of physiology found in the scientific literature. Some focus on what physiology is about—its object—whereas others focus on how physiology is used to study the biological reality—its method. Within each definition, we will examine the claims about the vitality of physiology. We will consider the specific features of physiology and whether it can continue to play the integrative role it has played in the past, with the capacity to unify diverse biological approaches and experimental data through common concepts or explanatory principles. The results of this conceptual investigation are shown in Table 1.Table 1 An examination of the most frequent definitions of the discipline of ‘physiology’ in the scientific literatureDefinition of Physiology in the LiteratureExplication of This DefinitionIs Physiology Alive in This Sense?MethodPhysiology is the science of functionsPhysiology focuses on identifying the causal contribution of a part to the whole organism.Alive but complemented by emerging biological disciplines not based on the explanation of biological phenomena through the assignment of causal roles.Physiology is the main explanatory domain of the biological sciencesIn this view, many life sciences are descriptive, but physiology is distinctive in that it aims to provide explanations of biological phenomena.Alive but complemented by emerging biological disciplines that do not provide explanations.Physiology is the basic science of organismsIn this view, biological data become intelligible only after their integration into a physiological framework.Alive since physiology is indeed a basic science based on a template of multiple layers of functions, but it is not necessarily the basic science in organism biology.ObjectPhysiology as the science of physiological and pathological phenomenaInsofar as it includes pathophysiology, physiology can be defined as the science of healthy and pathological phenomena.Alive and necessary, but not sufficient to explain how physiological phenomena become pathologicalPhysiology as the science of the integrity of the organismThis definition is understood in at least two senses:1) Physiology takes into account the organism as a whole when considering biological phenomena.2) Physiology investigates the role played by “unifying systems”—particularly the nervous and immune systems—in the integrity of the organism.Alive, but often vague. Physiological integration (in a hierarchy of embedded functions) must be complemented by other forms of integration. The nervous and immune systems are endowed with the capacity to unify the organism into a cohesive whole.Physiology as the science of a highly general, almost universal, biological process: the case of homeostasisPhysiology has focused on phenomena observable at all levels in all living beings, including homeostasis in particular.Alive but requiring complementation when the identification of interactions between physiological systems leads to the search for non-physiological explanations. Alive and fruitful when a homeostasis-based reasoning leads to the discovery of novel, “cross-system,” physiological phenomenon.Since it would be impossible to investigate systematically all published definitions of physiology, we tried to group together consensual and common views (left), especially in the context of the alleged crisis in physiology. We then used the philosophical method of conceptual analysis, or “explication,” to explain what these definitions refer to (middle). Finally, we propose a critical assessment of these definitions in terms of the vitality of physiology in modern science (right). One of the results of our analysis was the distinction between object-based (bottom) and method-based (top) definitions of physiology.In a nutshell, physiology can be viewed from two different angles. If we use a line of reasoning according to which each biological science provides its own contribution to the general functional explanation, then physiology now coexists with other disciplines. On the other hand, as a science with a specific object, the normal state of the whole organism, characterized by homeostasis, physiology is constantly reinventing itself and will continue to make a crucial contribution to other disciplines.What is Physiology? Lessons from the Historical Development of a DisciplinePhysiology has very deep, rich historical roots providing important insight into the current status of this discipline. A quick glance at the history of physiology highlights three key debates:Is physiology a general all-encompassing biological science, or, much more modestly, simply the medical investigation of the functions of human organs?Can a single, highly general phenomenon, such as homeostasis, serve as the basis for integrating knowledge about organisms?Can physiology be identified with a specific experimental method?The first of these debates concerns the status of physiology as either the broadest biological science or, much more humbly, a domain focusing primarily on humans and their health. Physiology has a long history. It has often been stressed that the roots of physiology lie in the works of Aristotle and Galen, and the term physiology was first coined by the French physician Jean Fernel in his De Naturali Parte Medicinae in 1542 (34). However, the meaning of physiology has changed significantly during the course of the history of this domain. In the 18th century, in particular, physiology had a broad, not specifically medical sense, encompassing animals and plants, very much like the modern term “biology” (114). This tradition culminated at the start of the 19th century with Dutrochet’s claim of the unification of the general science of physiology around phenomena such as osmosis (1). At around the same time, Schwann generalized the notion of metabolism, and both of these scientists promoted the idea of cellular physiology as a fundamental biological science applicable to all living things (28). Cuvier, through his conception of comparative anatomy based on functional correlations between organs, also contributed to this idea of a broad science (3), and “comparative physiology” developed in parallel with “comparative anatomy.” However, the term physiology has also been used in a more restricted, medical, and human-centered sense (22, 23), which has also undergone major shifts in meaning. Physiology was long considered a branch of anatomy (54), particularly at the institutional level, but also, to a lesser extent, intellectually. However, in the 18th and 19th centuries, physiologists began to show that function could not necessarily be deduced from structure (13), thereby relegating anatomy to an ancillary role (63, 114). This development led to a large number of physiology laboratories, departments, and societies being created in a general movement of liberation from both the anatomical and medical contexts. This debate about the object of physiology and its degree of generality (i.e., is its object limited to human health, or much more broadly, the entire living world?) is still alive today.The second debate concerns the possibility of using a single phenomenon as the unifying basis of physiology in general. Historically, physiologists endowed various phenomena with a central explanatory power in the general science of organisms. In the 18th century, living organisms were characterized by integrated mechanisms, systemic properties, or what was then called “living economy” and later became “animal economy” (114). This aspect was seen as the specific object of physiology at the beginning of the 19th century. By focusing on how organisms become autonomous with respect to variations of their environment, Claude Bernard defined the milieu intérieur, a basic phenomenon in every organism (6). Cannon stressed the importance of a dynamic equilibrium between essential parameters, which he referred to as homeostasis (15). These different views have in common the idea that it is possible to unify physiological processes under the banner of a single fundamental phenomenon of life. Again, as we will see below, many modern physiologists continue to share this ambition for their discipline (108).The third debate concerns the possibility of identifying physiology with a specific experimental method. Physiology became a fully fledged experimental science in the second half of the 19th century. At the time, physiology was firmly entrenched in a hypothesis-driven approach, promoted, in particular, by Claude Bernard (6, 8), considered by many to be the “founder” of experimental physiology (29, 43, 82), although other pioneers preceded him (42). One key question concerns the extent to which physiology can be identified with the use of what were then new, cutting-edge, specific detection and intervention techniques, such as electrophysiology or experimental lesions, as in the work of François Magendie, Johannes Müller, Claude Bernard, Herman von Helmoltz, Ivan Pavlov, and Charles Sherrington (63). Were the continual, rapid changes in technology accompanied by changes in physiology? Or did physiology remain associated with technologies invented at the end of the 19th and beginning of the 20th centuries? The influence of new experimental tools, transforming the field of physiology, continues to be a matter of debate for the physiologists of today (98).The definition of the discipline of physiology and estimations of its current relevance depend very much on which of these historical debates is considered the most important. Evaluation of the status of physiology in modern life sciences depends heavily on, for example, whether physiology is still seen as an all-encompassing discipline, whether it is seen as associated with a general phenomenon, such as homeostasis, or whether it is considered to be based on the use of specific experimental methods, such as electrophysiology. These different standpoints make it difficult to propose a general characterization of physiology, and at least some of the disagreements concerning the vitality of this discipline arise from the different conceptions of physiology held by different researchers.Despite these uncertainties, history suggests that a possible overall definition of physiology can be devised from its method and object (Table 2; see also Table 1). Such a definition would probably also be representative of the views of contemporary physiologists concerning their discipline. Methodologically speaking, physiology is explanatory, its explanations are of a functional kind, and it is integrative. Thematically, it focuses on phenomena considered normal or pathological, on the integrity of organisms or on general phenomena common to many or even all living things, such as homeostasis.Table 2 Characterization of physiology on the basis of its method and objectMethodObjectPhysiology is:Physiology is the science of:• An explanatory, as opposed to observational or predictive science• Normal and pathological phenomena• The science of functional explanations of living phenomena• The integrity of the organism• A basic science into which all the results of other biological sciences must ultimately be translatable• General phenomena common to many specialist fields in biologyBelow, we provide a detailed justification of this characterization of physiology in terms of its method and object, and we show that the current vitality of physiology can be assessed with reference to this classification.Physiological MethodsIn this section, we show that the primordial goal of physiology is explaining a system’s behavior, rather than predicting or controlling it, and that the explanations provided are based on function. Some recent, innovative approaches have diverged from this rationale of explanation based on function. It remains unclear whether these approaches should be seen as offshoots of physiology or of other disciplines. As we shall see, those inclined to see them as offshoots of physiology tend to view physiology as an integrative science, at the risk of reducing it to a synthesis of preexisting knowledge rather than a source of new knowledge.In this examination of the methods of physiology, we will begin by considering why attempts to explain phenomena on the basis of biological functions play such a key role in physiological science. We will then show that the relevance of physiology has been called into question precisely because emerging biological disciplines either do not explain biological phenomena in terms of function or do not explain them at all. Finally, we examine the claim, often made by physiologists themselves, that physiological methods remain the best way to integrate biological knowledge.The Central Role of Function in PhysiologyOne hallmark of physiology is its search for functional explanations. The identification of functions through their experimental neutralization provides information about the contribution of part of the organism to the whole, and an explanation of this function:“Successful physiological analysis requires an understanding of the functional interactions between the key components of cells, organs, and systems, as well as how these interactions change in disease states” (79).“Physiology, in my view, is clearly characterized by asking the truly functional questions. These questions can only be answered by continuously integrating knowledge from other disciplines into the larger scheme of mechanisms that allow organisms to actually live” (97).Philosophers of science have characterized “functional analysis” as the decomposition of a causal role of part of a system into a flowchart of functions (21). Functional analyses generally consider one of the effects or outputs of a system. They consider the causal interactions between parts, called “functions,” relative to the effect of interest. Each of these interactions can, in turn, be broken down into causal interactions between subparts. The result is an explanation. There is some debate among philosophers of biology and medicine as to whether this is sufficient to define a biological function (41). However, physiology has been based on such functional analyses since its inception. In our view, therefore, the most adequate definition of physiology is a science explaining functional organization.If this characterization of physiology is correct, then the strongest challenge to this domain is not the appearance of other experimental sciences but the recent emergence of both non-functional explanations and non-explanatory approaches in biology.Non-Functional Explanations of Biological PhenomenaInnovative approaches, such as systems biology, have recently provided explanations for biological phenomena that are not functional in nature. If such non-functional explanations are valid, then it would be overstretching the mark to suggest, as some have done, that systems biology, in its entirety, is just a new incarnation of physiology.Let us begin by considering one of the many examples of a non-functional explanation. The Gomperz-Makeham equation describes changes in the probability of death over time in a living organism: m(t) = I.eGt+ E, where I is intrinsic vulnerability, G is the rate of aging, and E represents environmental risk. G has been observed to be constant. Kowald recently proposed a simplified systems biology hypothesis concerning aging in which G is expressed in terms of mathematical functions describing the stochastic accumulation of mitochondrial defects (62).The explanandum (i.e., what is to be explained) is the change in the probability of death over time. The explanans (i.e., what the explanation is based on) is this mathematical function expressing the stochastic accumulation of defects. This explanation must be considered “non-functional” because it is not based on biological functions. Indeed, physiological functions, or at least their loss, instead define the explanandum.Philosophers have pointed out that systems biology sometimes resorts to explanations of functions by an explanans that is not itself a set of functions:“In a first approximation, systems biology may be said to study the interactions between the components of biological systems, and how they give rise to function and behavior by using a series of ‘omics’ operational protocols” (12).Moreover, one of the aims of systems biology is to decompartmentalize knowledge about the interactions occurring within physiologically defined systems performing particular functions, to achieve generalization to the interactions of various components of various systems, as highlighted by the philosophers O’Malley and Soyer (90). In this respect, systems biology contrasts with physiology, and with the major result of a long physiological tradition: the “breaking up” of the organism into well-delineated and functional “apparatuses” or “systems.” This tidy view of the concatenation of compartmentalized functional systems into a whole may, in some cases, hinder understanding of how organisms work. Along the same lines, the philosopher Philippe Huneman provided several examples of explanations of robustness—an essential property of biological systems at several levels, but not a function—in terms of topological properties (47). For instance, scale-free networks, in which a small number of nodes are highly connected and large numbers of nodes are poorly connected, are rarely disrupted by random mutations, which have an equal likelihood of striking any of the nodes of the network (4).Functional explanation is a crucial element in physiology. However, functional explanations, although not obsolete, naïve, or inadequate, are not the only possible explanations applicable to organisms. Non-functional explanations also exist and are increasing in importance in modern biology.Non-Explanatory Approaches in Modern BiologyThere has recently been an increase in the use of approaches that do not seek primarily to provide an explanation of the phenomenon considered but rather to predict and control it. This is particularly true of approaches based on systems biology and computer models. One of the many possible illustrations of this trend is provided by research on cancer treatments. In particular, “immunoscore,” expressing the degree of immune cell infiltration into the tumor, has recently been proposed as an alternative to the traditional TNM score, based on the presence of cancer cells in the tumor (T) and lymph node (N), and the presence of metastasis (M) (2). The advocates of immunoscore use have claimed that this score is superior to TNM for predicting disease outcome and treatment response for some cancers (37). This approach, which is based on systems biology, the use of complex computer models, bioinformatics, and big data (36), does not seek explanations in the way that physiology has traditionally done. More generally, approaches focusing on prediction and control rather than explanation have rapidly risen to the fore in many areas of biology and medicine over the last 10 years. These approaches can inspire, and be inspired by, physiology, but are not themselves physiological, in that they do not focus on explanation.Is Physiology the Basic Science of Organisms?In the eyes of many physiologists, non-physiological scientific results, such as those described above, acquire explanatory or predictive power only at the expense of clarity. According to this view, the findings of systems biology, for example, become meaningful and explanatory only when re-interpreted physiologically. The general idea is that systems biology provides tools for data collection, whereas only physiology can render the results intelligible. As Joyner put it:“. . . without a narrative approach that includes hypothesis testing and key concepts like homeostasis, systems biology runs the risk of becoming scientific ‘Abstract Expressionism’” (51).According to the defenders of this view, clarity can only be achieved by placing the knowledge gathered in non-physiological approaches into a framework, by integrating it into a physiological picture (52, 78, 79, 97). Without this integration into a physiological framework, biological claims cannot be correctly understood and explained. This is one of the implications of the notion that physiology is an integrative science and has been used to support the claim that physiology should be seen as the basic science of organisms.One argument that can be used in support of this view is that the functional template provided by physiology is not generally likely to be called into question by the results of non-physiological approaches. Indeed, in most cases, non-physiological approaches do not provide a novel functional explanation; they merely provide more detail and fill in gaps in our knowledge. This is what Noble calls the “boundary conditions” of the higher level on the lower level (82), meaning that results must be assimilated into a template at the organism level, just as the inner workings of ion channels cannot be understood without looking at the bigger picture of cell voltage.However, we think that this argument can be taken further since, in principle, there should always be a conceivable functional explanation of the phenomenon considered. The real question, therefore, is not so much whether physiology is a basic science but whether it is the basic science. The question thus boils down to what we consider to be ultimately clear or intelligible, which remains a matter of debate. As pointed out above, some would argue that systems biology provides intelligibility through mathematical models rather than functional templates (49), whereas others might claim that chains of chemical reactions or an evolutionary perspective also provide intelligibility without being based on function.There is no reason a priori to suppose that our understanding of what an organism does should necessarily involve the interplay of functions, or for assuming that anything the organism does could not be understood in this way. Thus physiology is indeed a basic science based on a template of multiple layers of functions, possibly encompassing all the knowledge about organisms collected, but it is not necessarily the basic science (i.e., the ultimate or most elementary science) in organism biology. As such, physiology is neither timeless nor outdated, because its descriptions of higher-level systems are not necessarily final and can, in principle, be modified in line with the results of data-intensive biology, certain phenomena may remain unexplained, and the descriptions generated are relevant for the organization of the information generated by this approach into a base of knowledge.Thus physiology is primarily defined by a specific approach, a functional, explanatory, and integrative approach. As such, physiology is alive and well, but it cannot be the all-encompassing discipline that it once was. Over the last decade, it has become increasingly clear that physiology must coexist with other approaches because it is not the only way to explain phenomena and because explanation need not be the sole goal of biology.Objects of PhysiologyWe will now turn our attention to definitions of physiology based on its object of investigation. What is the specific object of physiology, as opposed to other biological sciences? What we refer to here as the “object” of physiology is a highly general property of living beings forming a distinctive focus of interest for physiology. As reported in Table 2, this object has been defined in the physiological literature as “normal” as opposed to “pathological” processes, as the integrity of the organism as a whole, and as universal or quasi-universal biological processes, such as homeostasis. Below, we consider these three conceptions of the object of physiology.Physiology as the Science of Physiological and Pathological PhenomenaPhysiology has sometimes been defined as the science of healthy phenomena, and sometimes as the science of both healthy and pathological phenomena. This distinction, however, has been blurred by the emergence of molecular biology. Indeed, it is not always clear at the molecular level whether a phenomenon is “physiological” (normal) or “pathological” (abnormal). It has been suggested that this distinction is no longer relevant to the general science of living organisms. It has even been argued, by most philosophers of medicine (14, 19, 32, 87), with the notable exception of Christopher Boorse and some of his followers (10, 46), that this distinction is not grounded in hard science but merely reflects our values.This argument may be robust, but it does not necessarily imply that physiology has become dispensable or is a remnant of the past. Physiology remains a basic medical and biological science. Rough physiological descriptions of mechanisms serve as operational and objective proxies for our intuition that some states are “bad.” These states may be considered to be naturalized clinical entities, in that they provide a robust causal model of the basis for clinical manifestations of disease (64). When a molecular biologist scrutinizes complex processes, such as cascades of biochemical reactions, it is tacitly assumed that these processes are involved in physiological phenomena, pathological phenomena, or both, in that they can be causally linked to physiological or pathological, that is, biological processes, themselves known to underlie certain states or behaviors. We know what happens during fever, cardiac insufficiency, bronchial asthma, vomiting, diarrhea, cramps, fainting, headaches, and so on, although we do not always know why these phenomena occur. In philosophical terms, physiology is, in such cases, the science of the explanandum of molecular biology, that is, the prima facie biological phenomenon to be explained, rather than the science of the explanans, that is, the underlying processes explaining the phenomenon (see FIGURE 1).FIGURE 1.Levels of explanation (explanandum and explananda)Clinical phenomena (explandum) are first explained by physiological phenomena (explanans). These physiological phenomena (explandum) can then be explained by molecular phenomena (explanans) or by phenomena described by other innovative sciences.Download figureDownload PowerPointThus, as the science of the nonspecific phenomena explaining the states we deem normal or abnormal in daily life, physiology plays a key role in describing what requires further explanation, although the explanation is often obtained through other sciences, such as molecular biology.Physiology as the Science of the Integrity of the OrganismPhysiology has often been described as the science of whole organisms (15, 53, 93). According to this view, rather than being restricted to one particular biological level or organ, physiology involves the study of biological phenomena across all levels. This implies that physiological processes can occur at any level of organization in the organism, as testified by the existence of subfields such as “cellular physiology” (119) and “molecular physiology” (88). It also implies that physiology is “integrative,” in that it brings together knowledge accumulated about different body compartments (107). We suggest that physiology can be seen as “integrative” in two ways: “vertically” and “horizontally” (FIGURE 2; see also Ref. 117, p. 3).FIGURE 2.Physiology is both vertically (between different levels within an organ) and horizontally (between different organs) integrativeDownload figureDownload PowerPointPhysiology is “vertically integrative” in that it brings together knowledge about a given organ or system at different levels—genes, proteins, cells, tissues, etc, (66, 82). For example, a physiological account of the functioning of the heart requires an understanding of the roles of the entities located at differ" @default.
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W2805551057 title "Dissecting the Meanings of “Physiology” to Assess the Vitality of the Discipline" @default.
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