Medical explanations have often been thought on the model of biological ones and are frequently defined as mechanistic explanations of a biological dysfunction. In this paper, I argue that topological explanations, which have been described in ecology or in cognitive sciences, can also be found in medicine and I discuss the relationships between mechanistic and topological explanations in medicine, through the example of network medicine and medical genetics. Network medicine is a recent discipline that relies on the analysis of various (...) disease networks in order to find organizing principles in disease explanation. My aim is to show how topological explanations in network medicine can help solving the conceptual issues that pure mechanistic explanations of the genetics of disease are currently facing, namely the crisis of the concept of genetic disease, the progressive geneticization of diseases and the dissolution of the distinction between monogenic and polygenic diseases. However, I will also argue that topological explanations should not be considered as independent and radically different from mechanistic explanations for at least two reasons. First, in network medicine, topological explanations depend on and use mechanistic information. Second, they leave out some missing gaps in disease explanation that require, in turn, the development of new mechanistic explanations. Finally, I will insist on the specific contribution of topological explanations in medicine: they push us to develop an explanation of disease in general, instead of focusing on single explanations of individual diseases. This last point may have major consequences for biomedical research. (shrink)

Many explanations in science make use of mathematics. But are there cases where the mathematical component of a scientific explanation is explanatory in its own right? This issue of mathematical explanations in science has been for the most part neglected. I argue that there are genuine mathematical explanations in science, and present in some detail an example of such an explanation, taken from evolutionary biology, involving periodical cicadas. I also indicate how the answer to my title question impacts on broader (...) issues in the philosophy of mathematics; in particular it may help platonists respond to a recent challenge by Joseph Melia concerning the force of the Indispensability Argument. (shrink)

The Enhanced Indispensability Argument (Baker [ 2009 ]) exemplifies the new wave of the indispensability argument for mathematical Platonism. The new wave capitalizes on mathematics' role in scientific explanations. I will criticize some analyses of mathematics' explanatory function. In turn, I will emphasize the representational role of mathematics, and argue that the debate would significantly benefit from acknowledging this alternative viewpoint to mathematics' contribution to scientific explanations and knowledge.

In this paper I will reconstruct and analyze a famous argument by Stuart Kauffman about complex systems and evolution, in order to highlight the use in theoretical biology of a kind of non-mechanistic and non-causal explanation which I propose to call, following Kauffman, ensemble explanation. The aim is to contribute to the ongoing philosophical debate about non-causal explanations in the special sciences, kinds of explanation apparently extraneous to the received causal-mechanistic view. Ensemble explanations resemble quite closely the explanations of the (...) structural kind proposed by Philippe Huneman, which—unlike mechanistic explanations—do not explain by exposing the causal structure of a phenomenon, but... (shrink)

In this article, network science is discussed from a methodological perspective, and two central theses are defended. The first is that network science exploits the very properties that make a system complex. Rather than using idealization techniques to strip those properties away, as is standard practice in other areas of science, network science brings them to the fore, and uses them to furnish new forms of explanation. The second thesis is that network representations are particularly helpful in explaining the properties (...) of non-decomposable systems. Where part-whole decomposition is not possible, network science provides a much-needed alternative method of compressing information about the behavior of complex systems, and does so without succumbing to problems associated with combinatorial explosion. The article concludes with a comparison between the uses of network representation analyzed in the main discussion, and an entirely distinct use of network representation that has recently been discussed in connection with mechanistic modeling. (shrink)

In this paper, I discuss the prospects of nominalistic scientific realism and show that it fails on many counts. In section 2, I discuss what is required for NSR to get off the ground. In section 3, I question the idea that theories have well-defined nominalistic content and the idea that causal activity is a necessary condition for commitment to the reality of an entity. In section 4, I challenge the notion of nominalistic adequacy of theories.

This paper examines some recent attempts that use counterfactuals to understand the asymmetry of non-causal scientific explanations. These attempts recognize that even when there is explanatory asymmetry, there may be symmetry in counterfactual dependence. Therefore, something more than mere counterfactual dependence is needed to account for explanatory asymmetry. Whether that further ingredient, even if applicable to causal explanation, can fit non-causal explanation is the challenge that explanatory asymmetry poses for counterfactual accounts of non-causal explanation. This paper argues that several recent (...) accounts Explanation beyond causation: philosophical perspectives on non-causal explanations, Oxford University Press, Oxford, pp 117–140, 2018; Jansson and Saatsi in Br J Philos Sci, forthcoming; Jansson in J Philos 112:7–599, 2015; Saatsi and Pexton in Philos Sci 80: 613–624, 2013; French and Saatsi, in: Reutlinger and Saatsi Explanation beyond causation: philosophical perspectives on non-causal explanations, Oxford University Press, Oxford, pp 185–205, 2018) fail to meet this challenge. The paper then sketches a more positive proposal for dealing with explanatory asymmetry in non-causal explanations. (shrink)

In this paper, I argue that the newly developed network approach in neuroscience and biology provides a basis for formulating a unique type of realization, which I call topological realization. Some of its features and its relation to one of the dominant paradigms of realization and explanation in sciences, i.e. the mechanistic one, are already being discussed in the literature. But the detailed features of topological realization, its explanatory power and its relation to another prominent view of realization, namely the (...) semantic one, have not yet been discussed. I argue that topological realization is distinct from mechanistic and semantic ones because the realization base in this framework is not based on local realisers, regardless of the scale but on global realizers. In mechanistic approach, the realization base is always at the local level, in both ontic and epistemic accounts. The explanatory power of realization relation in mechanistic approach comes directly from the realization relation-either by showing how a model is mapped onto a mechanism, or by describing some ontic relations that are explanatory in themselves. Similarly, the semantic approach requires that concepts at different scales logically satisfy microphysical descriptions, which are at the local level. In topological framework the realization base can be found at different scales, but whatever the scale the realization base is global, within that scale, and not local. Furthermore, topological realization enables us to answer the “why” questions, which according to Polger 2010 make it explanatory. The explanatoriness of topological realization stems from understanding mathematical consequences of different topologies, not from the mere fact that a system realizes them. (shrink)

In this paper, I outline a heuristic for thinking about the relation between explanation and understanding that can be used to capture various levels of “intimacy”, between them. I argue that the level of complexity in the structure of explanation is inversely proportional to the level of intimacy between explanation and understanding, i.e. the more complexity the less intimacy. I further argue that the level of complexity in the structure of explanation also affects the explanatory depth in a similar way (...) to intimacy between explanation and understanding, i.e. the less complexity the greater explanatory depth and vice versa. (shrink)

In the last 20 years or so, since the publication of a seminal paper by Watts and Strogatz :440–442, 1998), an interest in topological explanations has spread like a wild fire over many areas of science, e.g. ecology, evolutionary biology, medicine, and cognitive neuroscience. The topological approach is still very young by all standards, and even within special sciences it still doesn’t have a single methodological programme that is applicable across all areas of science. That is why this special issue (...) is important as a first systematic philosophical study of topological explanations and their relation to a well understood and widespread explanatory strategy, such as mechanistic one. (shrink)

I argue that the hard problem of consciousness occurs only in very limited contexts. My argument is based on the idea of explanatory perspectivalism, according to which what we want to know about a phenomenon determines the type of explanation we use to understand it. To that effect the hard problem arises only in regard to questions such as how is it that concepts of subjective experience can refer to physical properties, but not concerning questions such as what gives rise (...) to qualia or why certain brain states have certain qualities and not others. In this sense we could for example fully explain why certain brain processes have certain subjective qualities, while we still don’t have a viable theory of concepts that explains co-referentiality of phenomenal and physical concepts. Given this limitation, the hard problem doesn’t pose a problem for the empirical study of consciousness. (shrink)

The problem of explanatory non-symmetries provides the strongest reason to abandon the view that laws can figure in explanations without causal underpinnings. I argue that this problem can be overcome. The solution that I propose starts from noticing the importance of conditions of application when laws do explanatory work, and I go on to develop a notion of nomological dependence that can tackle the non-symmetry problem. The strategy is to show how a strong notion of counterfactual dependence as guaranteed by (...) the laws is a plausible account of what we aim towards when we give law-based explanations. The aim of this project is not to deny that causal relations can do explanatory work but to restore laws of nature as capable of being explanatory even in the absence of any knowledge of causal underpinnings. (shrink)

This paper argues that besides mechanistic explanations, there is a kind of explanation that relies upon “topological” properties of systems in order to derive the explanandum as a consequence, and which does not consider mechanisms or causal processes. I first investigate topological explanations in the case of ecological research on the stability of ecosystems. Then I contrast them with mechanistic explanations, thereby distinguishing the kind of realization they involve from the realization relations entailed by mechanistic explanations, and explain how both (...) kinds of explanations may be articulated in practice. The second section, expanding on the case of ecological stability, considers the phenomenon of robustness at all levels of the biological hierarchy in order to show that topological explanations are indeed pervasive there. Reasons are suggested for this, in which “neutral network” explanations are singled out as a form of topological explanation that spans across many levels. Finally, I appeal to the distinction of explanatory regimes to cast light on a controversy in philosophy of biology, the issue of contingence in evolution, which is shown to essentially involve issues about realization. (shrink)

This paper argues that in some explanations mathematics are playing an explanatory rather than a representational role, and that this feature unifies many types of non-causal or non-mechanistic explanations that some philosophers of science have been recently exploring under various names. After showing how mathematics can play either a representational or an explanatory role by considering two alternative explanations of a same biological pattern—“Bergmann’s rule”—I offer an example of an explanation where the bulk of the explanatory job is done by (...) a mathematical theorem, and where mechanisms involved in the target systems are not explanatorily relevant. Then I account for the way mathematical properties may function in an explanatory way within an explanation by arguing that some mathematical propositions involving variables non directly referring to the target system features constitute constraints to which a whole class of systems should comply, provided they are describable by a mathematical object concerned by those propositions. According to such “constraint account”, those mathematical facts are directly entailing the explanandum, as a consequence of such constraints. I call those explanations “structural”, because here properties of mathematical structures are accounting for the explanandum; various kinds of mathematical structures thereby define various types of structural explanations. (shrink)

Stuart Kauffman here presents a brilliant new paradigm for evolutionary biology, one that extends the basic concepts of Darwinian evolution to accommodate recent findings and perspectives from the fields of biology, physics, chemistry and mathematics. The book drives to the heart of the exciting debate on the origins of life and maintenance of order in complex biological systems. It focuses on the concept of self-organization: the spontaneous emergence of order widely observed throughout nature. Kauffman here argues that self-organization plays an (...) important role in the emergence of life itself and may play as fundamental a role in shaping life's subsequent evolution as does the Darwinian process of natural selection. Yet until now no systematic effort has been made to incorporate the concept of self-organization into evolutionary theory. The construction requirements which permit complex systems to adapt remain poorly understood, as is the extent to which selection itself can yield systems able to adapt more successfully. This book explores these themes. It shows how complex systems, contrary to expectations, can spontaneously exhibit stunning degrees of order, and how this order, in turn, is essential for understanding the emergence and development of life on Earth. Topics include the new biotechnology of applied molecular evolution, with its important implications for developing new drugs and vaccines; the balance between order and chaos observed in many naturally occurring systems; new insights concerning the predictive power of statistical mechanics in biology; and other major issues. Indeed, the approaches investigated here may prove to be the new center around which biologicalscience itself will evolve. The work is written for all those interested in the cutting edge of research in the life sciences. (shrink)

Through his S–R model of statistical relevance, Wesley Salmon offers a solution to the scientific explanation of objectively improbable events.

As Aristotle stated, scientific explanation is based on deductive argument--yet, Wesley C. Salmon points out, not all deductive arguments are qualified explanations. The validity of the explanation must itself be examined. _Four Decades of Scientific Explanation_ provides a comprehensive account of the developments in scientific explanation that transpired in the last four decades of the twentieth century. It continues to stand as the most comprehensive treatment of the writings on the subject during these years. Building on the historic 1948 essay (...) by Carl G. Hempel and Paul Oppenheim, "Studies in the Logic of Explanation,” which introduced the deductive-nomological model on which most work on scientific explanation was based for the following four decades, Salmon goes beyond this model's inherent basis of describing empirical knowledge to tells us “not only _what,_ but also _why_.” Salmon examines the predominant models in chronological order and describes their development, refinement, and criticism or rejection. _Four Decades of Scientific Explanation_ underscores the need for a consensus of approach and ongoing evaluations of methodology in scientific explanation, with the goal of providing a better understanding of natural phenomena. (shrink)