Since the early 80s, metonymy has progressively gained central stage in linguistic investigations. The advent of cognitive linguistics marked a new turn in the study of this trope conceived, not as a deviation from semantic conventions (contra classical rhetorical theories), but as a phenomenon rooted in non-language-specific mechanisms of conceptualization and structuring of the world. Focusing on the particular case of whole-for-part (WP) metonymy, the general stand of this presentation will be to argue for the need to re-inject properly (...) semantic (descriptive and formal) considerations in the study of metonymy. It will be shown that semantic typologies of meronymic relations, as well as recent results in the semantics of partial predicates and colour predicates, can be jointly exploited to attain a better understanding of the mechanism of WP-metonymy. The resulting view will in particular connect such metonymies to mechanisms of reference and property attribution to functional parts for classificatory purposes. (shrink)

Although dual-process or divided-mind models of self-control dominate the literature, they suffer from empirical and conceptual challenges. We propose an alternative approach, suggesting that self-control can be characterized by a fragmented part versus integrated whole dynamic. Whereas responses to events derived from fragmented parts of the mind undermine self-control, responses to events derived from integrated wholes enhance self-control. We review empirical evidence from psychology and related disciplines that support this model. We, moreover, discuss the implications of this work (...) for psychology, neuroscience, economics, and philosophy. In particular, we highlight how this model addresses many of the conceptual and empirical short-comings of divided-mind models. We suggest that understanding self-control as the interplay between fragmented parts versus integrated wholes, moreover, provides novel insights and testable new hypotheses. (shrink)

A clever argument purports to show that we can directly perceive the emotions of others: (1) some emotional expressions are parts of the emotions they express; (2) perceiving a part of something is sufficient for perceiving the whole; (3) therefore, perceiving some emotional expressions is sufficient for perceiving the emotions they express. My aim in this paper is to assess the extent to which contemporary psychological theories of emotion support the first premise of this argument.

A scientific explanatory project, part-whole explanation, and a kind of science, part-whole science are premised on identifying, investigating, and using parts and wholes. In the biological sciences, mechanistic, structuralist, and historical explanations are part-whole explanations. Each expresses different norms, explananda, and aims. Each is associated with a distinct partitioning frame for abstracting kinds of parts. These three explanatory projects can be complemented in order to provide an integrative vision of the whole system, as is (...) shown for a detailed case study: the tetrapod limb. My diagnosis of part-whole explanation in the biological sciences as well as in other domains exploring evolved, complex, and integrated systems (e.g., psychology and cognitive science) cross-cuts standard philosophical categories of explanation: causal explanation and explanation as unification. Part-whole explanation is itself one essential aspect of part-whole science. (shrink)

Part–whole causation (PWC) is the thesis that some causes are part of their effects. PWC has been objected to because of its incompatibility with the criterion that causes not be spatially included within their effects and the criterion that causes and effects are ontologically distinct in some sense. This paper serves to undermine the sufficiency of these ways of objecting to PWC by showing that for each criterion either cause-effect relationships need not satisfy it or part–whole relationships can. (...) A case-study of the collapse of Bridge 9340 is employed to facilitate the discussion. (shrink)

The present article provides a mereological analysis of Euclid’s planar geometry as presented in the first two books of his Elements. As a standard of comparison, a brief survey of the basic concepts of planar geometry formulated in a set-theoretic framework is given in Section 2. Section 3.2, then, develops the theories of incidence and order using a blend of mereology and convex geometry. Section 3.3 explains Euclid’s “megethology”, i.e., his theory of magnitudes. In Euclid’s system of geometry, megethology takes (...) over the role played by the theory of congruence in modern accounts of geometry. Mereology and megethology are connected by Euclid’s Axiom 5: “The whole is greater than the part.” Section 4 compares Euclid’s theory of polygonal area, based on his “Whole-Greater-Than-Part” principle, to the account provided by Hilbert in his Grundlagen der Geometrie. An hypothesis is set forth why modern treatments of geometry abandon Euclid’s Axiom 5. Finally, in Section 5, the adequacy of atomistic mereology as a framework for a formal reconstruction of Euclid’s system of geometry is discussed. (shrink)

What are the conditions under which one biological object is a part of another biological object? This paper answers this question by developing a general, systematic account of biological parthood. I specify two criteria for biological parthood. Substantial Spatial Inclusionrequires biological parts to be spatially located inside or in the region that the natural boundary of t he biological whole occupies. Compositional Relevance captures the fact that a biological part engages in a biological process that must make a (...) necessary contribution to a condition that is minimally sufficient to one or more of the characteristic behaviors of the biological whole. Instead of emphasizing the diversity of part-whole relations in the biological world, this paper asks what biological part-whole relations have in common and what constrains their existence, in general. After presenting the two criteria for biological parthood I discuss in how far my account can cope with hard cases (e.g., redundant parts) and I reveal the merits and limits of monism. (shrink)

The approach adopted by Early Modern authors to the notions of ‘whole’ and ‘part’ (what is called, in contemporary metaphysics, “mereology”, from the Ancient Greek word μερος: ‘part’) constitutes a central feature of their respective systems. The issue of what constituted a whole became all the more crucial as the new, revolutionary approaches to matter and extension – which mark the unavoidably fuzzy beginning of what we define as “modernity” – demanded a novel (and in some cases, radical) (...) approach to the questions of what constitutes a whole and how parts are arranged and bound together. It is important to mention that diverse attitudes towards mereology characterised Early Modern philosophers orthogonally to their belonging to different camps, such as the traditional categories of ‘Rationalists’ and ‘Empiricists’. Some of these philosophers considered wholes to be ontologically and/or logically prior to their parts (an approach that we may call “organicist” or “holist”, applying an anachronistic but nonetheless appropriate label). Others considered wholes to be derivative, resulting from the union of their parts (an approach that could be named “mereological mechanism”). Therefore, a word about terminology is in order: in what follows, I will apply the label “holist/organicist” to refer to a philosopher who would favour the priority of wholes over parts. Vice versa, I shall label as a “mereological mechanist” any philosopher favouring the priority of parts over the wholes formed by those parts, regardless of such parts being exclusively material, or including spiritual/mental parts as well as material ones. (shrink)

ONE KIND OF PHILOSOPHICAL PUZZLEMENT arises when we have an apparent conflict of intuitions. If we are philosophers, we then try to show that the apparent conflict of intuitions is only an apparent conflict and not a real one. If we fail, we may have to say that what we took to be an apparent conflict of intuitions was in fact a conflict of apparent intuitions, and then we must decide which of the conflicting apparent intuitions is only an apparent (...) intuition. But if we succeed, then both of the intuitions will be preserved. Since there was an apparent conflict, we will have to conclude that the formulation of at least one of the intuitions was defective. And though the formulation may be imbedded in our ordinary language, we will have to say that, strictly and philosophically, a different formulation is to be preferred. But to make it clear that we are not rejecting the intuition we are reformulating, we must show systematically how to interpret the ordinary formulation into the philosophical one. The extent to which we can show this will be one mark of our success in dealing with the philosophical puzzle. Another will be the extent to which our proposed solution contributes to the solution of still other philosophical puzzles. (shrink)

Representing parthood relations in ORM has received little attention, despite its added-value of the semantics at the conceptual level. We introduce a high-level taxonomy of types of meronymic and mereological relations, use it to construct a decision procedure to determine which type of part- whole role is applicable, and incrementally add mandatory and uniqueness constraints. This enables the conceptual modeller to develop models that are closer to the real-world subject domain semantics, hence improve quality of the software.

The connection between whole and part is intimate: not only can we share the same space, but I’m incapable of leaving my parts behind; settle the nonmereological facts and you thereby settle what is a part of what; wholes don’t seem to be an additional ontological commitment over their parts. Composition as identity promises to explain this intimacy. But it threatens to make the connection too intimate, for surely the parts could have made a different (...) class='Hi'>whole and the whole have had different parts. In this paper I attempt to offer an account of parthood that is intimate enough but not too intimate: the parts generate the whole, but they are not themselves the whole. (shrink)

A taxonomy of part‐whole or meronymic relations is developed to explain the ordinary English‐speaker's use of the term “part of” and its cognates. The resulting classification yields six types of meronymic relations: 1. component‐integral object (pedal‐bike), 2. member‐collection (ship‐fleet), 3. portion‐mass (slice‐pie), 4. stuff‐object (steel‐car), 5. feature‐activity (paying‐shopping), and 6. place‐area (Everglades‐Florida). Meronymic relations ore further distinguished from other inclusion relations, such as spatial inclusion, and class inclusion, and from several other semantic relations: attribution, attachment, and ownership. This taxonomy (...) is then used to explain cases of apparent intransitivity in merological syllogisms, and standard form syllogisms whose premises express different inclusion relations. The data suggest that intransitivities arise due to equivocations between different types of semantic relations. These results are then explained by means of the relation element theory which accounts for the character and behavior of semantic relations in terms of more primitive relational elements. The inferential phenomena observed are then explained by means of a single principle of element matching. (shrink)

The relationship of part to whole is one of the most fundamental there is, yet until now there has been no full-length study of this concept. This book shows that mereology, the formal theory of part and whole, is essential to ontology. Peter Simons surveys and criticizes previous theories, especially the standard extensional view, and proposes a more adequate account which encompasses both temporal and modal considerations in detail. This has far-reaching consequences for our understanding of such classical (...) philosophical concepts as identity, individual, class, substance and accident, matter, form, essence, dependence, and integral whole. It also enables the author to offer new solutions to long-standing problems surrounding these concepts, such as the Ship of Theseus Problem and the issue of mereological essentialism. The author shows by his use of formal techniques that classical philosophical problems are amenable to rigorous treatment, and the book represents a synthesis of issues and methods from the analytical tradition and from the older continental realist tradition of Brentano and the early Husserl. (shrink)

Under what conditions are material objects, such as particles, parts of a whole object? This is the composition question and is a longstanding open question in philosophy. Existing attempts to specify a non-trivial restriction on composition tend to be vague and face serious counterexamples. Consequently, two extreme answers have become mainstream: composition (the forming of a whole by its parts) happens under no or all conditions. In this paper, we provide a self-contained introduction to the integrated (...) information theory of consciousness (IIT). We show that IIT specifies a non-trivial restriction on composition: composition happens when integrated information is maximized. We compare the IIT-restriction to existing proposals and argue that the IIT-restriction has significant advantages, especially in response to the problems of vagueness and counterexamples. An appendix provides an introduction to calculating parts and wholes with a simple system. (shrink)

In this paper, I suggest a way of resolving the whole-part dilemma suggested in the Parmenides. Specifically, I argue that grabbing the second horn of the dilemma does not pose a significant challenge. To argue for this, I consider two theses about Forms, namely, the oneness and indivisibility theses. More specifically, I argue that the second horn does not violate the oneness thesis if we treat composition as identity and that the indivisibility thesis ought to be reinterpreted given Plato’s (...) later dialogues. By doing so, I suggest a com-positional understanding of Plato’s theory of Forms, which can resolve the whole-part dilemma. (shrink)

BackgroundThe nature of a woman’s orgasm has been a source of scientific, political, and cultural debate for over a century. Since the Victorian era, the pendulum has swung from the vagina to the clitoris, and to some extent back again, with the current debate stuck over whether internal sensory structures exist in the vagina that could account for orgasms based largely on their stimulation, or whether stimulation of the external glans clitoris is always necessary for orgasm.MethodWe review the history of (...) the clitoral versus vaginal orgasm debate as it has evolved with conflicting ideas and data from psychiatry and psychoanalysis, epidemiology, evolutionary theory, feminist political theory, physiology, and finally neuroscience.ResultsA new synthesis is presented that acknowledges the enormous potential women have to experience orgasms from one or more sources of sensory input, including the external clitoral glans, internal region around the “G-spot” that corresponds to the internal clitoral bulbs, the c... (shrink)

I claim that a whole is identical to its parts. Many find this claim incredible: it seems that a whole and its parts must be distinct, for the whole is one thing while its parts are many things. Byeong-uk Yi has developed a version of this argument which exploits the resources of plural logic. Yi provides logical analyses of the predicates ‘one’ and ‘many’ which seem to show that nothing can satisfy them both. But (...) there are two senses of the word ‘one’. One of these senses is not captured by Yi’s analysis, and in this sense of the word, it is logically possible for many things to be one. Moreover, we should only believe that a whole is one thing in this sense, not that it is one thing in the sense Yi has analysed. Thus, we can identify wholes with their parts without contradiction. (shrink)

In the visual representation of ontologies, in particular of part-whole relationships, it is customary to use graph theory as the representational background. We claim here that the standard graph-based approach has a number of limitations, and we propose instead a new representation of part-whole structures for ontologies, and describe the results of experiments designed to show the effectiveness of this new proposal especially as concerns reduction of visual complexity. The proposal is developed to serve visualization of ontologies conformant (...) to the Basic Formal Ontology. But it can be used also for more general applications, particularly in the biomedical domain. (shrink)

Material objects extend through space by having different spatial parts in different places. But how do they persist through time? According to some philosophers, things have temporal parts as well as spatial parts: accepting this is supposed to help us solve a whole bunch of metaphysical problems, and keep our philosophy in line with modern physics. Other philosophers disagree, arguing that neither metaphysics nor physics give us good reason to believe in temporal parts.

Several disputes about the nature of experience operate under the assumption that experiences have parts, including temporal parts. There's the widely held view, when it comes to temporal experiences, that we should follow James' exhortation that such experiences aren't mere successions of their temporal parts, but something more. And there's the question of whether it is the parts of experiences which determine whole experiences and the properties they have, or whether the determination goes instead from (...) the whole to the parts, as holists have it. But what are parts, or temporal parts, of experiences exactly—what does it mean to say that an experience is “part” of another? Are the participants in those disputes talking about the same thing—is there a univocal notion of “experiential part” available? Are there different kinds of experiential parts? And if there are, is there a systematic way of carving them out? More importantly, how should we conceive of the temporal parts of experiences, and how can we establish that experiences really do have temporal parts, against those who reject the notion? (shrink)

Understanding the organization of an organism by individuating meaningful parts and accounting for organismal properties by studying the interaction of bodily parts is a central practice in many areas of biology. While structures are obvious bodily parts and structure and function have often been seen as antagonistic principles in the study of organismal organization, my tenet is that structures and functions are on a par. I articulate a notion of function (functions as activities), according to which functions (...) are bodily parts just as structures are. Recognizing part-whole relations among an organism’s various structures and functions permits fruitful investigation and multilevel explanation of organismal properties and functioning, across both developmental and evolutionary time. I show how my perspective clarifies debates surrounding homology and evolutionary novelty that stem from an alleged structure-function dichotomy. My approach favors a pluralism about individuation, where the criteria of what counts as a meaningful bodily part depend on the particular epistemic aims pursued in a scientific context. (shrink)

I use Carl Gillett’s much heralded dimensioned theory of realization as a platform to develop a plausible part–whole theory. I begin with some basic desiderata for a theory of realization that its key terms should be defined and that it should be explanatory. I then argue that Gillett’s original theory violates these conditions because its explanatory force rests upon an unspecified “in virtue of” relation. I then examine Gillett’s later version that appeals instead to theoretical terms tied to “mechanisms.” (...) Yet I argue that it too violates the desiderata, since it defines realization for mechanisms in terms of two undefined ideas whose explanatory credentials have not been established—“implementation” and “grounds.” Thus I drop those ideas in favor of an explicit constraint that the parts and properties provide a mechanistic explanation. I also distinguish a special mechanistic theory from a preferred general theory that incorporates other kinds of part–whole explanations that target causal powers or capacities. The result is a theory that has the explanatory virtues of mechanistic theories as well as a broader scope desired by Gillett. I also compare the result to a similar idea from Robert Cummins that has been neglected in recent discussions of realization, namely, his general property analysis rather than his functional analysis. Finally, I defend the preferred general theory against possible objections that attempt to show a conflict between metaphysical demands on a theory of realization versus facts about good scientific explanation. (shrink)

The relationship of part to whole is one of the most fundamental there is; this is the first and only full-length study of this concept. This book shows that mereology, the formal theory of part and whole, is essential to ontology. Peter Simons surveys and criticizes previous theories, especially the standard extensional view, and proposes a more adequate account which encompasses both temporal and modal considerations in detail. 'Parts could easily be the standard book on mereology for (...) the next twenty or thirty years.' Timothy Williamson, Grazer Philosophische Studien. (shrink)

In this paper (the second of two parts) we propose a structural interpretation of Schröder’s work, pointing out his insistence on the priority of a whole in comparison with its parts. The examples are taken from the diverse areas in which Schröder was active, with a particular interest in his project of an absolute algebra.

Abstract In this paper I propose a mereological account of ordinary macro-events of experience that is based on two central features of these entities, namely their spatio-temporal character, and their status as things that belong to event-kinds. I argue that, from the perspective of descriptive metaphysics, these features must be incorporated in the analysis of the part-whole relations of events, and I show the steps involved in achieving this task. Furthermore, I argue that the program initiated here is quite (...) promising: the analysis of event-part that I propose stands up quite well against the more serious objections, and the apparatus I provide for the mereological conditions of events can be easily modified to yield similar conditions for material objects. (shrink)

Many philosophers today accept that phenomenal truths cannot be explained in terms of ordinary physical truths. Two possible routes to accounting for consciousness have received much attention: the emergentist route is to accept that ordinary experience is inexplicable in physical terms but that microscopic entities as described in physics nonetheless bring about conscious experience. The second route is to argue that microscopic entities have features not described in physics which can fully explain conscious experience. The view associated with panprotopsychism is (...) that microscopic entities have no phenomenal properties. The view associated with panpsychism is that microscopic entities do have phenomenal properties. In this paper it is argued that if consciousness is extended in space only the latter view is possible. According to this argument for micropsychism, if phenomenal truths are not merely structural, all truths about a whole are truths about its parts plus structural relational truths. If there are phenomenal truths about the whole, this must be because there are phenomenal truths about its parts. It wouldn’t follow that panpsychism is true, since it does not follow that consciousness exists outside the wholes we know to be conscious, but it does follow that emergentism and protopanpsychism are false. (shrink)

The dominant theory of parts and wholes – classical extensional mereology – has faced a number of challenges in the recent literature. This article gives a sampling of some of the alleged counterexamples to some of the more controversial principles involving the connections between parthood and identity. Along the way, some of the main revisionary approaches are reviewed. First, counterexamples to extensionality are reviewed. The ‘supplementation’ axioms that generate extensionality are examined more carefully, and a suggested revision is considered. (...) Second, the paper considers an alternative approach that focuses the blame on antisymmetry but allows us to keep natural supplementation axioms. Third, we look at counterexamples to the idempotency of composition and the associated ‘parts just once’ principle. We explore options for developing weaker mereologies that avoid such commitments. (shrink)

Deep convolutional networks exceed humans in sensitivity to local image properties, but unlike biological vision systems, do not discover and encode abstract relations that capture important properties of objects and events in the world. Coupling network architectures with additional machinery for encoding abstract relations will make deep networks better models of human abilities and more versatile and capable artificial devices.

In De ciuitate Dei (ciu.), Augustine famously calls people with disabilities created on purpose by an absolutely competent God (16.8). On the whole, however, Augustine's views on disabilities in ciu. are often misunderstood. The statement about the creation of people with disabilities is part of a discussion of the theodicy question that implies that the goodness of people with disabilities is not open to experience and must be accepted on faith. This negative background assumption results from Augustine's view that (...) dignity emerges from the embodied beauty, rationality, and utility of the ensouled body (22). Augustine gives several examples of how disabilities reduce dignity along with these dimensions, as “deformity defeats beauty” (19.4). In eternal salvation, however, disabilities will be removed (22). Martyrs will perhaps retain scars in heaven, but these particular scars will be of such a kind that there is “not deformitas in them, but dignitas” (22.19). If in the resurrection for eternal life God removes congenital disabilities that God created so competently, what is their purpose in the first place? Augustine regards disabilities as temporal embodied warnings of eternal corporeal punishment (21.8). As a concluding perspective, the alternative view of disabilities by the Apostle Paul will be considered. (shrink)

Adolescents are said to be, figuratively speaking, thin-skinned. But their thin-skinnedness is also real: both ambivalent and ambiguous, the border between self and other is, for many young people, a source of constant turmoil. The recourse to bodily self-harm is a means of dealing with this turmoil and the feelings of powerlessness it generates. Drawing on extensive semi-structured interviews conducted over the course of the last twenty years, this article explores the experiences of adolescents who engage in self-cutting. A deliberate (...) and controlled use of pain, this ‘symbolic homeopathy’ – that is, harming oneself to feel less pain – acts as a defence against externally imposed suffering. Far from being destructive, self-harm practices can paradoxically be understood as survival techniques. Part of a long-term, ongoing project investigating adolescent risk-taking, this article seeks to better understand the experiences of teens who injure themselves through skin-cutting. (shrink)

This paper presents a theory of algorithms designed to optimize highly interactive systems (multi-diminsional, multi-peak, nonlinear functions). Two applications are discussed: one concerns cognitive systems capable of learning and generalization, and one concerns calculations dealing with the "origin of life" from "organic soups". The algorithms are intrinsically parallel--each function argument processed serves as a carrier for information about a tremendous number of regions (hyperplanes) in the function's domain. Each region is automatically ranked according to the estimated average value of the (...) function over that region, and the rankings are compactly stored in the algorithm's data base (M l-tuples store approximately M-2 l/2 rankings). Thus, the algorithm implicitly processes hyperplanes by manipulating function arguments. (shrink)

Two kinds of explanation might be put forward. The first goes like this: the necessary connection between the location of a whole and the location of its parts holds because the location of the whole is nothing but the collective location of its parts. The second style of explanation goes like this: the connection holds because what it is for a material whole to have something as a part, is (perhaps among other things) for the (...) whole to contain the part. (shrink)

This paper examines whether classical extensional mereology is adequate for formalizing the whole–parts relation in quantum chemical systems. Although other philosophers have argued that classical extensional and summative mereology does not adequately formalize whole–parts relation within organic wholes and social wholes, such critiques often assume that summative mereology is appropriate for formalizing the whole–parts relation in inorganic wholes such as atoms and molecules. However, my discussion of atoms and molecules as they are conceptualized in (...) quantum chemistry will establish that standard mereology cannot adequately fulfill this task, since the properties and behavior of such wholes are context-dependent and cannot simply be reduced to the summative properties of their parts. To the extent that philosophers of chemistry have called for the development of an alternative mereology for quantum chemical systems, this paper ends by proposing behavioral mereology as a promising step in that direction. According to behavioral mereology, considerations of what constitutes a part of a whole is dependent upon the observable behavior displayed by these entities. Thus, relationality and context-dependence are stipulated from the outset and this makes behavioral mereology particularly well-suited as a mereology of quantum chemical wholes. The question of which mereology is appropriate for formalizing the whole–parts relation in quantum chemical systems is relevant to contemporary philosophy of chemistry, since this issue is related to the more general questions of the reducibility of chemical wholes to their parts and of the reducibility of chemistry to physics, which have been of central importance within the philosophy of chemistry for several decades. More generally, this paper puts contemporary discussions of mereology within the philosophy of chemistry into a broader historical and philosophical context. In doing so, this paper also bridges the gap between formal mereology, conceived as a branch of formal ontology, and “applied” mereology, conceived as a branch of philosophy of science. (shrink)

How can the power of wholes be resisted without essentializing their parts? Drawing on different archives and methodologies, including aesthetics, history, biology, affect, race, and queer, the interventions in this volume explore different ways of troubling the consistency and stability of wholes, breaking up their closure and making them more dynamic. Doing so without necessarily presupposing or producing parts, an outside, or a teleological development, they indicate the critical potential of partiality without parts.

Many of us think that ordinary objects – such as tables and chairs – exist. We also think that ordinary objects have parts: my chair has a seat and some legs as parts, for example. But once we are committed to the (seemingly innocuous) thesis that ordinary objects are composed of parts, we then open ourselves up to a whole host of philosophical problems, most of which center on what exactly the composition relation is. Composition as (...) Identity (CI) is the view that the composition relation is the identity relation. While such a view has some advantages, there are many arguments against it. In this essay, I will briefly canvass three different varieties of Composition as Identity, and suggest why one of them should be preferred over the others. Then I will outline several versions of the most common objection against CI. I will suggest how a CI theorist can respond to these charges by maintaining that some of the arguments are invalid. (In part 2, I show how a CI theorist can maintain that the remaining arguments, while valid, are unsound). (shrink)

Many of us think that ordinary objects – such as tables and chairs – exist. We also think that ordinary objects have parts: my chair has a seat and some legs as parts, for example. But once we are committed to the (seemingly innocuous) thesis that ordinary objects are composed of parts, we then open ourselves up to a whole host of philosophical problems, most of which center on what exactly this composition relation is. Composition as (...) Identity (CI) is the view that the composition relation is the identity relation. While such a view has some advantages, there are many arguments against it. In this essay, I discuss several versions of the most common objection against CI, and show how the CI theorist can maintain that these arguments – contrary their initial intuitive appeal – are nonetheless unsound. (shrink)

Systems biologists often distance themselves from reductionist approaches and formulate their aim as understanding living systems “as a whole.” Yet, it is often unclear what kind of reductionism they have in mind, and in what sense their methodologies would offer a superior approach. To address these questions, we distinguish between two types of reductionism which we call “modular reductionism” and “bottom-up reductionism.” Much knowledge in molecular biology has been gained by decomposing living systems into functional modules or through detailed (...) studies of molecular processes. We ask whether systems biology provides novel ways to recompose these findings in the context of the system as a whole via computational simulations. As an example of computational integration of modules, we analyze the first whole-cell model of the bacterium M. genitalium. Secondly, we examine the attempt to recompose processes across different spatial scales via multi-scale cardiac models. Although these models rely on a number of idealizations and simplifying assumptions as well, we argue that they provide insight into the limitations of reductionist approaches. Whole-cell models can be used to discover properties arising at the interfaces of dynamically coupled processes within a biological system, thereby making more apparent what is lost through decomposition. Similarly, multi-scale modeling highlights the relevance of macroscale parameters and models and challenges the view that living systems can be understood “bottom-up.” Specifically, we point out that system-level properties constrain lower-scale processes. Thus, large-scale modeling reveals how living systems at the same time are more and less than the sum of the parts. (shrink)