This chapter contains sections titled: Introduction A Brief History of Developmental Explanations of Phenotypic Evolution Research Questions of Evo‐Devo Unifying Themes of the Conceptual Basis of Evo‐Devo Conclusion: A Mechanistic Theory of Evo‐Devo Challenges the Modern Synthesis Postscript: Counterpoint References.

My goal in this paper is to provide characterizations of matter, form and constituency in a way that avoids what I take to be the three main drawbacks of other hylomorphic theories: (i) commitment to the universal-particular distinction; (ii) commitment to a primitive or problematic notion of inherence or constituency; (iii) inability to identify viable candidates for matter and form in nature, or to characterize them in terms of primitives widely regarded to be intelligible.

Here I present and discuss a model that, among other things, appears able to describe the dynamics of cancer cell origin from the perspective of stable and unstable gene expression profiles. In identifying suchaberrantgene expression profiles as lying outside the normal stable states attracted through development and normal cell differentiation, the hypothesis explains why cancer cells accumulate mutations, to which they are not robust, and why these mutations create a new stable state far from the normal gene expression profile space. (...) Such cells are in strong contrast with normal cell types that appeared as an attractor state in the gene expression dynamical system under cell‐cell interaction and achieved robustness to noise through evolution, which in turn also conferred robustness to mutation. In complex gene regulation networks, otheraberrantcellular states lacking such high robustness are expected to remain, which would correspond to cancer cells. (shrink)

In this important study D. M. Armstrong offers a comprehensive system of analytical metaphysics that synthesises but also develops his thinking over the last twenty years. Armstrong's analysis, which acknowledges the 'logical atomism' of Russell and Wittgenstein, makes facts the fundamental constituents of the world, examining properties, relations, numbers, classes, possibility and necessity, dispositions, causes and laws. All these, it is argued, find their place and can be understood inside a scheme of states of affairs. This is a comprehensive and (...) rigorously this-worldly account of the most general features of reality, argued from a distinctive philosophical perspective, and it will appeal to a wide readership in analytical philosophy. (shrink)

It is a familiar point that many ordinary dispositions are multi-track, that is, not fully and adequately characterisable by a single conditional. In this paper, I argue that both the extent and the implications of this point have been severely underestimated. First, I provide new arguments to show that every disposition whose stimulus condition is a determinable quantity must be infinitely multi-track. Secondly, I argue that this result should incline us to move away from the standard assumption that dispositions are (...) in some way importantly linked to conditionals, as presupposed by the debate about various versions of the ‘conditional analysis’ of dispositions. I introduce an alternative conception of dispositionality, which is motivated by linguistic observations about dispositional adjectives and links dispositions to possibility instead of conditionals. I argue that, because of the multi-track nature of dispositions, the possibility-based conception of dispositions is to be preferred. (shrink)

This paper presents a counterfactual account of what a mechanism is. Mechanisms consist of parts, the behavior of which conforms to generalizations that are invariant under interventions, and which are modular in the sense that it is possible in principle to change the behavior of one part independently of the others. Each of these features can be captured by the truth of certain counterfactuals.

Most philosophical accounts of emergence are incompatible with reduction. Most scientists regard a system property as emergent relative to properties of its parts if it depends upon their mode of organization-a view consistent with reduction. Emergence is a failure of aggregativity, in which ``the whole is nothing more than the sum of its parts''. Aggregativity requires four conditions, giving powerful tools for analyzing modes of organization. Differently met for different decompositions of the system, and in different degrees, the structural conditions (...) can provide evaluation criteria for choosing decompositions, ``natural kinds'', and detecting functional localization fallacies, approximations, and various biases of vulgar reductionisms. This analysis of emergence and use of these conditions as heuristics is consistent with a broader reductionistic methodology. (shrink)

According to Aristotelian essentialism, the nature of an organism is constituted of a particular goal-directed disposition to produce an organism typical of its kind. This paper argues—against the prevailing orthodoxy—that essentialism of this sort is indispensable to evolutionary biology. The most powerful anti-essentialist arguments purport to show that the natures of organisms play no explanatory role in modern synthesis biology. I argue that recent evolutionary developmental biology provides compelling evidence to the contrary. Developmental biology shows that one must appeal to (...) the capacities of organisms to explain what makes adaptive evolution adaptive. Moreover, the specific capacities in question are precisely those that, according to Aristotle, constitute the nature of an organism. Essentialism 1.1 Aristotelian biological kinds Evolutionary anti-essentialism 2.1 Taxonomic anti-essentialism 2.2 Explanatory anti-essentialism Adaptation 3.1 Stability 3.2 Mutability 3.3 Phenotypic plasticity and adaptive evolution The natures of organisms Conclusion. (shrink)

This paper argues for a broadly dispositionalist approach to the ontology of Bohmian mechanics . It first distinguishes the ‘minimal’ and the ‘causal’ versions of Bohm’s theory, and then briefly reviews some of the claims advanced on behalf of the ‘causal’ version by its proponents. A number of ontological or interpretive accounts of the wave function in BM are then addressed in detail, including configuration space, multi-field, nomological, and dispositional approaches. The main objection to each account is reviewed, namely the (...) ‘problem of perception’, the ‘problem of communication’, the ‘problem of temporal laws’, and the ‘problem of under-determination’. It is then shown that a version of dispositionalism overcomes the under-determination problem while providing neat solutions to the other three problems. A pragmatic argument is thus furnished for the use of dispositions in the interpretation of the theory more generally. The paper ends in a more speculative note by suggesting ways in which a dispositionalist interpretation of the wave function is in addition able to shed light upon some of the claims of the proponents of the causal version of BM. (shrink)

In recent years, a significant number of philosophers from an orthodox analytic background have begun to advocate theories of composite objects, which they say are strikingly similar to Aristotle’s hylomorphism. These theories emphasize the importance of structure, or organization—which they say is closely connected to Aristotle’s notion of form—in defining what it is for a composite to be a genuine object. The reality of these structures is closely connected with the fact that they are held to possess powers, again in (...) what is held to be a broadly Aristotelian sense, and so to be genuinely efficacious. Naturally enough, they want to do all this without espousing the discredited aspects of Aristotelian science. It is the purpose of this essay to cast a skeptical eye on whether this objective can be achieved. (shrink)

summaryMartin and Pfeifer have claimed“that the most typical characterizations of intentionality… all fail to distinguish … mental states from …dispositional physical states.”The evidence they present in support of this thesis is examined in the light of the possibility that what it shows is that intentionality is the mark, not of the mental, but of the dispositional. Of the five marks of intentionality they discuss a critical examination shows that three of them, Brentano's inexistence of the intentional object, Searle's directedness and (...) Anscombe's indeterminacy, are features which distinguish T‐inten Tional/dispositional The other two are either, as in the case of Chisholm's permissible falsity of a propositional attitude ascription, a feature of linguistic utterances too restricted in its scope to be of interest, or, as in the case of Frege's indirect reference/Quine's referential opacity, evidence that the S‐intenSional locution is a quotation either of what someone has said in the past or might be expected to say, if the question were to arise at some time in the future. (shrink)

1. Consider a circle. It has both a radius and a circumference. There is obviously a real distinction between the properties having a radius and having a circumference. This is not because, when confining ourselves to circles,1 having a radius can ever exist apart from having a circumference. A real distinction does not depend on that. Descartes thought that a real distinction between x and y meant that x could exist without y or vice versa, if only by the power (...) of God. But Descartes was wrong. Separable existence is a sufficient but not necessary condition of there being a real distinction. The difference between a real and a conceptual distinction derives from medieval philosophy. Aquinas, for one, held that things can be really distinct even though not separable (the form and matter of a material substance or its essence and existence, for example).2 For a merely conceptual distinction between x and y to exist, it is necessary for the distinction to exist in thought only. There is only a conceptual distinction between an upward slope and a downward slope, or between a glass’s being half empty and half full. Not only are the members of such pairs inseparable (whether by God or in any other way), but there is no real distinction between them. There is no numerical distinctness between the entities or qualities between which there is only a conceptual distinction. To this extent alone is Galen Strawson (2008) correct.3 But when it comes to.. (shrink)

The distinction between the essence of an object and its properties has been obscured in contemporary discussion of essentialism. Locke held that the properties of an object are exclusively those features that ‘flow’ from its essence. Here he follows the Aristotelian theory, leaving aside Locke’s own scepticism about the knowability of essence. I defend the need to distinguish sharply between essence and properties, arguing that essence must be given by form and that properties flow from form. I give a precise (...) definition of what the term of art ‘flow’ amounts to, and apply the distinction to various kinds of taxonomic issues. (shrink)

The concept of mechanism in biology has three distinct meanings. It may refer to a philosophical thesis about the nature of life and biology (‘mechanicism’), to the internal workings of a machine-like structure (‘machine mechanism’), or to the causal explanation of a particular phenomenon (‘causal mechanism’). In this paper I trace the conceptual evolution of ‘mechanism’ in the history of biology, and I examine how the three meanings of this term have come to be featured in the philosophy of biology, (...) situating the new ‘mechanismic program’ in this context. I argue that the leading advocates of the mechanismic program (i.e., Craver, Darden, Bechtel, etc.) inadvertently conflate the different senses of ‘mechanism’. Specifically, they all inappropriately endow causal mechanisms with the ontic status of machine mechanisms, and this invariably results in problematic accounts of the role played by mechanism-talk in scientific practice. I suggest that for effective analyses of the concept of mechanism, causal mechanisms need to be distinguished from machine mechanisms, and the new mechanismic program in the philosophy of biology needs to be demarcated from the traditional concerns of mechanistic biology. (shrink)

This paper defends wave function realism against the charge that the view is empirically incoherent because our evidence for quantum theory involves facts about objects in three-dimensional space or space-time . It also criticizes previous attempts to defend wave function realism against this charge by claiming that the wave function is capable of grounding local beables as elements of a derivative ontology.

Teller argued that violations of Bell’s inequalities are to be explained by interpreting quantum entangled systems according to ‘relational holism’, that is, by postulating that they exhibit irreducible (‘inherent’) relations. Teller also suggested a possible application of this idea to quantum statistics. However, the basic proposal was not explained in detail nor has the additional idea about statistics been articulated in further work. In this article, I reconsider relational holism, amending it and spelling it out as appears necessary for a (...) proper assessment, and application, of the position. †To contact the author, please write to: FB Philosophie‐Zukunftskolleg, University of Konstanz, Universitätstraße 10, 78464, Konstanz, Germany; e‐mail: matteo.morganti@uni ‐konstanz.de. (shrink)

George Molnar came to see that the solution to a number of the problems of contemporary philosophy lay in the development of an alternative to Hume's metaphysics. This alternative would have real causal powers at its centre. Molnar set about developing a thorough account of powers that might persuade those who remained, perhaps unknowingly, in the grip of Humean assumptions. He succeeded in producing something both highly focused and at the same time wide-ranging. He showed both that the notion of (...) a power was central and that it could serve to dispel a number of long-standing philosophical problems.Molnar's account of powers is as realist as any that has so far appeared. He shows that dispositions are as real as any other properties. Specifically, they do not depend for their existence on their manifestations. Nevertheless, they are directed towards such manifestations. Molnar thus appropriates the notion of intentionality, from Brentano, and argues that it is the essential characteristic of powers. He offers a persuasive case for there being some basic and ungrounded powers, thus ruling out the reducibility of the dispositional to the non-dispositional. However, he does allow that there are non-power properties as well as power properties. In this respect, his final position is dualistic.This is contemporary metaphysics of the highest quality. It is a work that was almost complete when its author died. It has been edited for publication by another specialist in the subject, Stephen Mumford, who has also provided an introduction that will allow non-specialists to become acquainted with the issues. David Armstrong, one of the greatest living metaphysicians and personal friend of George Molnar, has provided a Foreword. (shrink)

Philosophical accounts of emergence have been explicated in terms of logical relationships between statements (derivation) or static properties (function and realization). Jaegwon Kim is a modern proponent. A property is emergent if it is not explainable by (or reducible to) the properties of lower level components. This approach, I will argue, is unable to make sense of the kinds of emergence that are widespread in scientific explanations of complex systems. The standard philosophical notion of emergence posits the wrong dichotomies, confuses (...) compositional physicalism with explanatory physicalism, and is unable to represent the type of dynamic processes (self-organizing feedback) that both generate emergent properties and express downward causation. (shrink)

To determine whether dispositions are causally relevant, we have to get clear about what causal relevance is. Several characteristics of causal relevance have been suggested, including Explanatory Power, Counterfactual Dependence, Lawfullness, Exclusion, Independence, and Minimal Sufficiency. Different accounts will yield different answers about the causal relevance of dispositions. However, accounts of causal relevance that are the most plausible, for independent reasons, render the verdict that dispositions are causally relevant.

Degeneracy is a poorly understood process, essential to natural selection. In the 18th and 19th centuries, the concept of degeneracy was commandeered by the colonial imagination. A rigid understanding of species, race, and culture grew to dominate the normative thinking that persisted well into the burgeoning new industrial age. A 20th-century reconfiguration of the concept by George Gamow highlighted a form of intraorganismic variation that is still underexplored. Degeneracy exists in a population of variants where structurally different components perform a (...) similar, but not necessarily identical, function with respect to context. The presence of degeneracy increases a system’s complexity and robustness against perturbations. The loss of a genetic component in biological systems, for example, can be compensated by redundant elements , or by degenerate elements . A historical survey of the use of the term “degeneracy” reveals how and why the processes it once designated, and the mechanisms it now represents, have largely escaped the purview of contemporary science. Despite confusion and general oversight, degeneracy has been characterized by select researchers at the molecular, genetic, and neuronal levels. The concept is a potent analytical tool to understand selection, variation, and transmission. (shrink)

What are the most fundamental features of the world? Do minds stand outside the natural order? Is a unified picture of mental and physical reality possible? The Mind in Nature provides a staunchly realist account of the world as a unified system incorporating both the mental and the physical.

The Mind in Nature has two central aims. First, that of defending a ‘basic ontology’. Second, having advanced a plausible ontological framework, to appeal to it to cast light on the status of intentionality and the nature of consciousness, paying particular attention to the question of what distinguishes conscious systems from those that are vegetative.Central to Martin's basic ontology is his acceptance of a realist conception of dispositionality. Contrary to the view of David Lewis and others, talk about a thing's (...) dispositions cannot be analysed as talk about a thing's behaviour in a set of counterfactual circumstances. The account of dispositions that emerges from Martin's discussion is one according to which a specific disposition is either actual or it is not. To be actual a disposition need not be manifesting any manifestation. Unmanifesting dispositions are not, therefore, unactualized possibilia – a description which, he observes, is more fitting of unmanifested manifestations. In advancing a realist conception of dispositionality, Martin also opposes those who maintain that dispositional properties reduce to …. (shrink)

Analyses of dispositional ascriptions in terms of conditional statements famously confront the problems of finks and masks. We argue that conditional analyses of dispositions, even those tailored to avoid finks and masks, face five further problems. These are the problems of: (i) Achilles' heels, (ii) accidental closeness, (iii) comparatives, (iv) explaining context sensitivity, and (v) absent stimulus conditions. We conclude by offering a proposal that avoids all seven of these problems.

The concept of mechanism is analyzed in terms of entities and activities, organized such that they are productive of regular changes. Examples show how mechanisms work in neurobiology and molecular biology. Thinking in terms of mechanisms provides a new framework for addressing many traditional philosophical issues: causality, laws, explanation, reduction, and scientific change.

The goal of this paper is to encourage a reconfiguration of the discussion about typology in biology away from the metaphysics of essentialism and toward the epistemology of classifying natural phenomena for the purposes of empirical inquiry. First, I briefly review arguments concerning ‘typological thinking’, essentialism, species, and natural kinds, highlighting their predominantly metaphysical nature. Second, I use a distinction between the aims, strategies, and tactics of science to suggest how a shift from metaphysics to epistemology might be accomplished. Typological (...) thinking can be understood as a scientific tactic that involves representing natural phenomena using idealizations and approximations, which facilitates explanation, investigation, and theorizing via abstraction and generalization. Third, a variety of typologies from different areas of biology are introduced to emphasize the diversity of this representational reasoning. One particular example is used to examine how there can be epistemological conflict between typology and evolutionary analysis. This demonstrates that alternative strategies of typological thinking arise due to the divergent explanatory goals of researchers working in different disciplines with disparate methodologies. I conclude with several research questions that emerge from an epistemological reconfiguration of typology. (shrink)

Many years ago, C.B. Martin drew our attention to the possibility of ‘finkish’ dispositions: dispositions which, if put to the test would not be manifested, but rather would disappear. Thus if x if finkishly disposed to give response r to stimulus s, it is not so that if x were subjected to stimulus r, x would give response z; so finkish dispositions afford a counter‐example to the simplest conditional analysis of dispositions. Martin went on to suggest that finkish dispositions required (...) a theory of primitive causal powers; there, I think, he was mistaken. All that they require is an improved conditional analysis, and this improved analysis can be built upon whatever treatments of properties and of laws we may favour on other grounds. (shrink)

Proponents of mechanistic explanation all acknowledge the importance of organization. But they have also tended to emphasize specificity with respect to parts and operations in mechanisms. We argue that in understanding one important mode of organization—patterns of causal connectivity—a successful explanatory strategy abstracts from the specifics of the mechanism and invokes tools such as those of graph theory to explain how mechanisms with a particular mode of connectivity will behave. We discuss the connection between organization, abstraction, and mechanistic explanation and (...) illustrate our claims by looking at an example from recent research on so-called network motifs. (shrink)

A staunch hylomorphism involves a commitment to a sparse theory of universals and a sparse theory of composite material objects, as well as to an ontology of fundamental causal powers. Faint-hearted hylomorphism, in contrast, lacks one or more of these elements. On the staunch version of HM, a substantial form is not merely some structural property of a set of elements—it is rather a power conferred on those elements by that structure, a power that is the cause of the generation (...) (by fusion) and persistence of a composite whole through time. Bernard Williams discussed (and rejected) a faint-hearted version of HM in 1986, and faint-hearted HM has been defended more recently by Mark Johnston (2006) and Kathrin Koslicki (2008). I defend the superiority of the staunch version, in spite of its heavier ontological commitments, as a way of accounting for a real distinction between living organisms and heaps of matter, without recourse to dualism or vitalism, and as a way of combining a powers ontology with the possibility of gunk. (shrink)

We argue that dynamical and mathematical models in systems and cognitive neuro- science explain (rather than redescribe) a phenomenon only if there is a plausible mapping between elements in the model and elements in the mechanism for the phe- nomenon. We demonstrate how this model-to-mechanism-mapping constraint, when satisfied, endows a model with explanatory force with respect to the phenomenon to be explained. Several paradigmatic models including the Haken-Kelso-Bunz model of bimanual coordination and the difference-of-Gaussians model of visual receptive fields are (...) explored. (shrink)

Recently, it has been provocatively claimed that dynamical modeling approaches signal the emergence of a new explanatory framework distinct from that of mechanistic explanation. This paper rejects this proposal and argues that dynamical explanations are fully compatible with, even naturally construed as, instances of mechanistic explanations. Specifically, it is argued that the mathematical framework of dynamics provides a powerful descriptive scheme for revealing temporal features of activities in mechanisms and plays an explanatory role to the extent it is deployed for (...) this purpose. It is also suggested that more attention should be paid to the distinctive methodological contributions of the dynamical framework including its usefulness as a heuristic for mechanism discovery and hypothesis generation in contemporary neuroscience and biology. (shrink)

With the advent of evolutionary developmental research, or EvoDevo, there is hope of discovering the roles that the genetic bases of development play in morphological evolution. Studies in EvoDevo span several levels of organismal organization. Low-level studies identify the ultimate genetic changes responsible for morphological variation and diversity. High-level studies of development focus on how genetic differences affect the dynamics of gene networks and epigenetic interactions to modify morphology. Whereas an increasing number of studies link independent acquisition of homoplastic or (...) convergent morphologies to similar changes in the genomes, homoplasies are not always found to have identical low-level genetic underpinnings. This suggests that a combination of low- and high-level approaches may be useful in understanding the relationship between genetic and morphological variation. Therefore, as an empirical and conceptual framework, we propose the causality horizon to signify the lowest level that allows linking homoplastic morphologies to similar changes in the development. A change in a system below the causality horizon cannot be generalized. In more concrete terms, homoplastic morphologies cannot be reduced to the same change in gene regulation when that change occurs below the causality horizon; rather, a higher-level mechanism should be identified. (shrink)

“Hylomorphism” has recently become a buzzword in metaphysics. Kit Fine, Kathryn Koslicki, and Mark Johnston, among others, have argued that hylomorphism provides an account of parthood and material constitution that has certain advantages over its competitors. But what exactly is it, and what are its implications for an account of what we are? Hylomorphism, I argue, is fundamentally a claim about structure. It says that structure is a basic ontological and explanatory principle. I argue that hylomorphism is compatible with physicalism, (...) and also with substance dualism, and epiphenomenalism. The most interesting kinds of hylomorphism nevertheless reject these views. I describe one such hylomorphic theory. It is an empirically well-warranted theory, I argue, one based on work in biology and biological subdisciplines such as neuroscience. (shrink)

“Hylomorphism” has recently become a buzzword in metaphysics. Kit Fine, Kathryn Koslicki, and Mark Johnston, among others, have argued that hylomorphism provides an account of parthood and material constitution that has certain advantages over its competitors. But what exactly is it, and what are its implications for an account of what we are? Hylomorphism, I argue, is fundamentally a claim about structure. It says that structure is a basic ontological and explanatory principle. I argue that hylomorphism is compatible with physicalism, (...) and also with substance dualism, and epiphenomenalism. The most interesting kinds of hylomorphism nevertheless reject these views. I describe one such hylomorphic theory. It is an empirically well-warranted theory, I argue, one based on work in biology and biological subdisciplines such as neuroscience. (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)

The Neo‐Darwinian concept of natural selection is plausible when one assumes a straightforward causation of phenotype by genotype. However, such simple 1:1 mapping must now give place to the modern concepts of gene regulatory networks and gene expression noise. Both can, in the absence of genetic mutations, jointly generate a diversity of inheritable randomly occupied phenotypic states that could also serve as a substrate for natural selection. This form of epigenetic dynamics challenges Neo‐Darwinism. It needs to incorporate the non‐linear, stochastic (...) dynamics of gene networks. A first step is to consider the mathematical correspondence between gene regulatory networks and Waddington's metaphoric ‘epigenetic landscape’, which actually represents the quasi‐potential function of global network dynamics. It explains the coexistence of multiple stable phenotypes within one genotype. The landscape's topography with its attractors is shaped by evolution through mutational re‐wiring of regulatory interactions – offering a link between genetic mutation and sudden, broad evolutionary changes. (shrink)

The stunning possibility of “reprogramming” differentiated somatic cells to express a pluripotent stem cell phenotype (iPS, induced pluripotent stem cell) and the “ground state” character of pluripotency reveal fundamental features of cell fate regulation that lie beyond existing paradigms. The rarity of reprogramming events appears to contradict the robustness with which the unfathomably complex phenotype of stem cells can reliably be generated. This apparent paradox, however, is naturally explained by the rugged “epigenetic landscape” with valleys representing “preprogrammed” attractor states that (...) emerge from the dynamical constraints of the gene regulatory network. This article provides a pedagogical primer to the fundamental principles of gene regulatory networks as integrated dynamic systems and reviews recent insights in gene expression noise and fate determination, thereby offering a formal framework that may help us to understand why cell fate reprogramming events are inherently rare and yet so robust. (shrink)