According to one large family of views, scientific explanations explain a phenomenon (such as an event or a regularity) by subsuming it under a general representation, model, prototype, or schema (see Bechtel, W., & Abrahamsen, A. (2005). Explanation: A mechanist alternative. Studies in History and Philosophy of Biological and Biomedical Sciences, 36(2), 421–441; Churchland, P. M. (1989). A neurocomputational perspective: The nature of mind and the structure of science. Cambridge: MIT Press; Darden (2006); Hempel, C. G. (1965). Aspects of scientific (...) explanation. In C. G. Hempel (Ed.), Aspects of scientific explanation (pp. 331–496). New York: Free Press; Kitcher (1989); Machamer, P., Darden, L., & Craver, C. F. (2000). Thinking about mechanisms. Philosophy of Science, 67(1), 1–25). My concern is with the minimal suggestion that an adequate philosophical theory of scientific explanation can limit its attention to the format or structure with which theories are represented. The representational subsumption view is a plausible hypothesis about the psychology of understanding. It is also a plausible claim about how scientists present their knowledge to the world. However, one cannot address the central questions for a philosophical theory of scientific explanation without turning one’s attention from the structure of representations to the basic commitments about the worldly structures that plausibly count as explanatory. A philosophical theory of scientific explanation should achieve two goals. The first is explanatory demarcation. It should show how explanation relates with other scientific achievements, such as control, description, measurement, prediction, and taxonomy. The second is explanatory normativity. It should say when putative explanations succeed and fail. One cannot achieve these goals without undertaking commitments about the kinds of ontic structures that plausibly count as explanatory. Representations convey explanatory information about a phenomenon when and only when they describe the ontic explanations for those phenomena. (shrink)

What is the best account of process reliabilism about epistemic justification, especially epistemic entitlement? I argue that entitlement consists in the normal functioning (proper operation) of the belief-forming process when the process has forming true beliefs reliably as an etiological function. Etiological functions involve consequence explanation: a belief-forming process has forming true beliefs reliably as a function just in case forming-true beliefs reliably partly explains the persistence of the process. This account paves the way for avoiding standard objections to process (...) reliabilism and situations epistemic entitlement within a normative framework of functions and functional norms. (shrink)

In this paper, we develop an organizational account that defines biological functions as causal relations subject to closure in living systems, interpreted as the most typical example of organizationally closed and differentiated self-maintaining systems. We argue that this account adequately grounds the teleological and normative dimensions of functions in the current organization of a system, insofar as it provides an explanation for the existence of the function bearer and, at the same time, identifies in a non-arbitrary way the norms that (...) functions are supposed to obey. Accordingly, we suggest that the organizational account combines the etiological and dispositional perspectives in an integrated theoretical framework. IntroductionDispositional ApproachesEtiological TheoriesBiological Self-maintenance Closure, teleology, and normativityOrganizational differentiationFunctions C1: Contributing to the maintenance of the organization C2: Producing the functional trait Implications and Objections Functional versus useful Dysfunctions, side effects, and accidental contributionsProper functions and selected effectsReproductionRelation with other ‘unitarian’ approachesConclusions. (shrink)

In a recent paper, Kaplan (Synthese 183:339–373, 2011) takes up the task of extending Craver’s (Explaining the brain, 2007) mechanistic account of explanation in neuroscience to the new territory of computational neuroscience. He presents the model to mechanism mapping (3M) criterion as a condition for a model’s explanatory adequacy. This mechanistic approach is intended to replace earlier accounts which posited a level of computational analysis conceived as distinct and autonomous from underlying mechanistic details. In this paper I discuss work in (...) computational neuroscience that creates difficulties for the mechanist project. Carandini and Heeger (Nat Rev Neurosci 13:51–62, 2012) propose that many neural response properties can be understood in terms of canonical neural computations. These are “standard computational modules that apply the same fundamental operations in a variety of contexts.” Importantly, these computations can have numerous biophysical realisations, and so straightforward examination of the mechanisms underlying these computations carries little explanatory weight. Through a comparison between this modelling approach and minimal models in other branches of science, I argue that computational neuroscience frequently employs a distinct explanatory style, namely, efficient coding explanation. Such explanations cannot be assimilated into the mechanistic framework but do bear interesting similarities with evolutionary and optimality explanations elsewhere in biology. (shrink)

This paper offers an account of what it is for a physical system to be a computing mechanism—a system that performs computations. A computing mechanism is a mechanism whose function is to generate output strings from input strings and (possibly) internal states, in accordance with a general rule that applies to all relevant strings and depends on the input strings and (possibly) internal states for its application. This account is motivated by reasons endogenous to the philosophy of computing, namely, doing (...) justice to the practices of computer scientists and computability theorists. It is also an application of recent literature on mechanisms, because it assimilates computational explanation to mechanistic explanation. The account can be used to individuate computing mechanisms and the functions they compute and to taxonomize computing mechanisms based on their computing power. (shrink)

In this paper, I defend a new theory of normative reasons called reasons as good bases, according to which a normative reason to φ is something that is a good basis for φing. The idea is that the grounds on which we do things—bases—can be better or worse as things of their kind, and a normative reason—a good reason—is something that is just a good instance of such a ground. After introducing RGB, I clarify what it is to be a (...) good basis, and argue that RGB has various attractive features: it has intuitive implications, makes good sense of the weights of reasons, and attractively explains the relationship between normative reasons and motivating reasons. I then briefly defend the view from objections and compare it to rivals. Finally, I sketch two possible implications of RGB: some kind of constitutivism, according to which the norms that govern us are explained by the nature of agency, and second, the claim that agents who do things for reasons generally do them for good reasons. (shrink)

This paper reviews the debate on the notion of biological function and on functional explanation as this takes place in philosophy. It describes the different perspectives, issues, intuitions, theories and arguments that have emerged. The author shows that the debate has been too heavily influenced by the concerns of a naturalistic philosophy of mind and argues that in order to improve our understanding of biology the attention should be shifted from the study of intuitions to the study of the actual (...) practice of biological inquiry. (shrink)

Though nativist hypotheses have played a pivotal role in the development of cognitive science, it remains exceedingly obscure how they—and the debates in which they figure—ought to be understood. The central aim of this paper is to provide an account which addresses this concern and in so doing: a) makes sense of the roles that nativist theorizing plays in cognitive science and, moreover, b), explains why it really matters to the contemporary study of cognition. I conclude by outlining a range (...) of further implications of this account for current debate in cognitive science. (shrink)

I present an account of mental representation based upon the ‘SINBAD’ theory of the cerebral cortex. If the SINBAD theory is correct, then networks of pyramidal cells in the cerebral cortex are appropriately described as representing, or more specifically, as modelling the world. I propose that SINBAD representation reveals the nature of the kind of mental representation found in human and animal minds, since the cortex is heavily implicated in these kinds of minds. Finally, I show how SINBAD neurosemantics can (...) provide accounts of misrepresentation, equivocal representation, twin cases, and Frege cases. (shrink)

I defend the view that many biological categories are defined by homology against a series of arguments designed to show that all biological categories are defined, at least in part, by selected function. I show that categories of homology are `abnormality inclusive'—something often alleged to be unique to selected function categories. I show that classifications by selected function are logically dependent on classifications by homology, but not vice-versa. Finally, I reject the view that biologists must use considerations of selected function (...) to abstract away from variation and pathology to form a canonical description of a class of biological systems. (shrink)

Defending or attacking either functionalism or computationalism requires clarity on what they amount to and what evidence counts for or against them. My goal here is not to evaluate their plausibility. My goal is to formulate them and their relationship clearly enough that we can determine which type of evidence is relevant to them. I aim to dispel some sources of confusion that surround functionalism and computationalism, recruit recent philosophical work on mechanisms and computation to shed light on them, and (...) clarify how functionalism and computationalism may or may not legitimately come together. (shrink)

I analyze the importance of parts in the style of biological theorizing that I call compositional biology. I do this by investigating various aspects, including partitioning frames and explanatory accounts, of the theoretical perspectives that fall under and are guided by compositional biology. I ground this general examination in a comparative analysis of three different disciplines with their associated compositional theoretical perspectives: comparative morphology, functional morphology, and developmental biology. I glean data for this analysis from canonical textbooks and defend the (...) use of such texts for the philosophy of science. I end with a discussion of the importance of recognizing formal and compositional biology as two genuinely different ways of doing biology – the differences arising more from their distinct methodologies than from scientific discipline included or natural domain studied. Ultimately, developing a translation manual between the two styles would be desirable as they currently are, at times, in conflict. (shrink)

Numerous research groups are now utilizing Basic Formal Ontology as an upper-level framework to assist in the organization and integration of biomedical information. This paper provides elucidation of the three existing BFO subcategories of realizable entity, namely function, role, and disposition. It proposes one further sub-category of tendency, and considers the merits of recognizing two sub-categories of function for domain ontologies, namely, artifactual and biological function. The motivation is to help advance the coherent ontological treatment of functions, roles, and dispositions, (...) to help provide the potential for more detailed classification, and to shed light on BFO’s general make-up and use. (shrink)

According to pancomputationalism, everything is a computing system. In this paper, I distinguish between different varieties of pancomputationalism. I find that although some varieties are more plausible than others, only the strongest variety is relevant to the philosophy of mind, but only the most trivial varieties are true. As a side effect of this exercise, I offer a clarified distinction between computational modelling and computational explanation.<br><br>.

“Functional homology” appears regularly in different areas of biological research and yet it is apparently a contradiction in terms—homology concerns identity of structure regardless of form and function. I argue that despite this conceptual tension there is a legitimate conception of ‘homology of function’, which can be recovered by utilizing a distinction from pre-Darwinian physiology (use versus activity) to identify an appropriate meaning of ‘function’. This account is directly applicable to molecular developmental biology and shares a connection to the theme (...) of hierarchy in homology. I situate ‘homology of function’ within existing definitions and criteria for structural assessments of homology, and introduce a criterion of ‘organization’ for judging function homologues, which focuses on hierarchically interconnected interdependencies (similar to relative position and connection for skeletal elements in structural homology). This analysis of biological concepts has at least three broad philosophical consequences: (1) it provides the grounds for the study of behavior and psychological categories as homologues; (2) it demonstrates that philosophers who take selected effect function as primary effectively ignore large portions of comparative, structural, and experimental research, thereby misconstruing biological reasoning and knowledge; and, (3) it underwrites causal generalizations, which illuminates inferences made from model organisms in experimental biology. (shrink)

Functional language is ubiquitous in ecology, mainly in the researches about biodiversity and ecosystem function. However, it has not been adequately investigated by ecologists or philosophers of ecology. In the contemporary philosophy of ecology we can recognize a kind of implicit consensus about this issue: while the etiological approaches cannot offer a good concept of function in ecology, Cummins’ systemic approach can. Here we propose to go beyond this implicit consensus, because we think these approaches are not adequate for ecology. (...) We argue that a sound epistemological framework to function in ecology is to be found in organizational approaches. In this line, we define function in ecology as a precise effect of a given constraint on the ecosystem flow of matter and energy performed by a given item of biodiversity, within a closure of constraints. We elaborate on this definition by developing a case study of a bromeliad ecosystem. (shrink)

A biochemical pathway is a sequence of chemical reactions in a biological organism. Such pathways specify mechanisms that explain how cells carry out their major functions by means of molecules and reactions that produce regular changes. Many diseases can be explained by defects in pathways, and new treatments often involve finding drugs that correct those defects. This paper presents explanation schemas and treatment strategies that characterize how thinking about pathways contributes to biomedical discovery. It discusses the significance of pathways for (...) understanding the nature of diseases, explanations, and theories. (shrink)

This is a short overview of the biological functions debate in philosophy. While it was fairly comprehensive when it was written, my short book ​A Critical Overview of Biological Functions has largely supplanted it as a definitive and up-to-date overview of the debate, both because the book takes into account new developments since then, and because the length of the book allowed me to go into substantially more detail about existing views.

I offer an explication of the notion of computer, grounded in the practices of computability theorists and computer scientists. I begin by explaining what distinguishes computers from calculators. Then, I offer a systematic taxonomy of kinds of computer, including hard-wired versus programmable, general-purpose versus special-purpose, analog versus digital, and serial versus parallel, giving explicit criteria for each kind. My account is mechanistic: which class a system belongs in, and which functions are computable by which system, depends on the system's mechanistic (...) properties. Finally, I briefly illustrate how my account sheds light on some issues in the history and philosophy of computing as well as the philosophy of mind. (shrink)

I consider some hitherto unexplored examples of teleological language in the sciences. In explicating these examples, I aim to show (a) that such language is not the sole preserve of the biological sciences, and (b) that not all such talk is reducible to the ascription of functions. In chemistry and biochemistry, scientists explaining molecular rearrangements and protein folding talk informally of molecules rearranging “in order to” maximize stability. Evolutionary biologists, meanwhile, often speak of traits evolving “in order to” optimize some (...) fitness-relevant variable. I argue that in all three contexts such locutions are best interpreted as shorthands for more detailed explanations which, were we to spell them out in full, would show that the relevant process would robustly converge towards the same end-point despite variation in initial conditions. This suggests that, in biology, such talk presupposes a substantial form of adaptationism. The upshot is that such shorthands may be more applicable in the physical sciences than the biological. (shrink)

John is currently thinking that the sun is bright. Consider his occurrent belief or judgement that the sun is bright. Its content is that the sun is bright. This is a truth- evaluable content (which shall be our main concern) because it is capable of being true or false. In virtue of what natural, scientifically accessible facts does John’s judgement have this content? To give the correct answer to that question, and to explain why John’s judgement and other contentful mental (...) states have the contents they do in virtue of such facts, would be to naturalize mental content. (shrink)

Evolution in its contemporary meaning in biology typically refers to the changes in the proportions of biological types in a population over time (see the entry on the concept of evolution to 1872 for earlier meanings). As evolution is too large of a topic to address thoroughly in one entry, the primary goal of this entry is to serve as a broad overview of contemporary issues in evolution with links to other entries where more in-depth discussion can be found. The (...) entry begins with a brief survey of definitions of evolution, followed by a discussion of the different modes of evolution and related philosophical issues, and ends with a summary of other topics in the philosophy of evolution focusing particularly on topics covered in this encyclopedia. (shrink)

Two controversies exist regarding the appropriate characterization of hierarchical and adaptive evolution in natural populations. In biology, there is the Wright-Fisher controversy over the relative roles of random genetic drift, natural selection, population structure, and interdemic selection in adaptive evolution begun by Sewall Wright and Ronald Aylmer Fisher. There is also the Units of Selection debate, spanning both the biological and the philosophical literature and including the impassioned group-selection debate. Why do these two discourses exist separately, and interact relatively little? (...) We postulate that the reason for this schism can be found in the differing focus of each controversy, a deep difference itself determined by distinct general styles of scientific research guiding each discourse. That is, the Wright-Fisher debate focuses on adaptive process, and tends to be instructed by the mathematical modeling style, while the focus of the Units of Selection controversy is adaptive product, and is typically guided by the function style. The differences between the two discourses can be usefully tracked by examining their interpretations of two contested strategies for theorizing hierarchical selection: horizontal and vertical averaging. (shrink)

Discussions of the functions of biological traits generally take the notion of a trait for granted. Defining this notion is a non-trivial problem. Different approaches to function place different constraints on adequate accounts of the notion of a trait. Accounts of function based on engineering-style analyses allow trait boundaries to be a matter of human interest. Accounts of function based on natural selection have typically been taken to require trait boundaries that are objectively real. After canvassing problems raised by each (...) approach, I conclude with some facts that satisfactory notions of trait must respect. (shrink)

This PhD dissertation examines the conceptual and theoretical foundations of the most general and most widely used framework for understanding social evolution, W. D. Hamilton's theory of kin selection. While the core idea is intuitive enough (when organisms share genes, they sometimes have an evolutionary incentive to help one another), its apparent simplicity masks a host of conceptual subtleties, and the theory has proved a perennial source of controversy in evolutionary biology. To move towards a resolution of these controversies, we (...) need a careful and rigorous analysis of the philosophical foundations of the theory. My aim in this work is to provide such an analysis. I begin with an examination of the concepts behavioural ecologists employ to describe and classify types of social behaviour. I stress the need to distinguish concepts that are often conflated: for example, we need to distinguish simple cooperation from collaboration in collective tasks, behaviours from strategies, and control from manipulation and coercion. I proceed from here to the formal representation of kin selection via George R. Price’s covariance selection mathematics. I address a number of interpretative issues the Price formalism raises, including the vexed question of whether kin selection theory is ‘formally equivalent’ to multi-level selection theory. In the second half of the dissertation, I assess the uses and limits of Hamilton’s rule for the evolution of social behaviour; I provide a precise statement of the conditions under which the rival neighbour-modulated fitness and inclusive fitness approaches in contemporary kin selection theory are equivalent (and describe cases in which they are not); and I criticize recent formal attempts to establish the controversial claim that kin selection leads to organisms behaving as if maximizing their inclusive fitness. (shrink)

In an illuminating article, Claus Beisbart argues that the recently-popular thesis that the probabilities of statistical mechanics (SM) are Best System chances runs into a serious obstacle: there is no one axiomatization of SM that is robustly best, as judged by the theoretical virtues of simplicity, strength, and fit. Beisbart takes this 'no clear winner' result to imply that the probabilities yielded by the competing axiomatizations simply fail to count as Best System chances. In this reply, we express sympathy for (...) the 'no clear winner' thesis. However, we argue that an importantly different moral should be drawn from this. We contend that the implication for Humean chances is not that there are no SM chances, but rather that SM chances fail to be sharp. (shrink)

In this note some epistemological problems in general theories about living systems are considered; in particular, the question of hidden connections between different areas of experience, such as folk biology and scientific biology, and hidden connections between central concepts of theoretical biology, such as function, semiosis, closure and life.

Externalist analyses of justification typically include some sort of reliability requirement. But the fact that the beliefs of a demon victim can be justified despite their being formed in completely unreliable ways suggests that reliability isn’t required for justification. In this paper, I propose an analysis of justification in terms of proper function that enables us to hang on to the externalism without the reliability requirement. As an added bonus, the proposed analysis of justification yields an account of the elusive (...) connection between justification and truth. (shrink)

This paper investigates the concept of behavioral autonomy in Artificial Life by drawing a parallel to the use of teleological notions in the study of biological life. Contrary to one of the leading assumptions in Artificial Life research, I argue that there is a significant difference in how autonomous behavior is understood in artificial and biological life forms: the former is underlain by human goals in a way that the latter is not. While behavioral traits can be explained in relation (...) to evolutionary history in biological organisms, in synthetic life forms behavior depends on a design driven by a research agenda, further shaped by broader human goals. This point will be illustrated with a case study on a synthetic life form. Consequently, the putative epistemic benefit of reaching a better understanding of behavioral autonomy in biological organisms by synthesizing artificial life forms is subject to doubt: the autonomy observed in such artificial organisms may be a mere projection of human agency. Further questions arise in relation to the need to spell out the relevant human aims when addressing potential social or ethical implications of synthesizing artificial life forms. (shrink)

This paper proposes a basic revision of the understanding of teleology in biological sciences. Since Kant, it has become customary to view purposiveness in organisms as a bias added by the observer; the recent notion of teleonomy expresses well this as-if character of natural purposes. In recent developments in science, however, notions such as self-organization (or complex systems) and the autopoiesis viewpoint, have displaced emergence and circular self-production as central features of life. Contrary to an often superficial reading, Kant gives (...) a multi-faceted account of the living, and anticipates this modern reading of the organism, even introducing the term self-organization for the first time. Our re-reading of Kant in this light is strengthened by a group of philosophers of biology, with Hans Jonas as the central figure, who put back on center stage an organism-centered view of the living, an autonomous center of concern capable of providing an interior perspective. Thus, what is present in nuce in Kant, finds a convergent development from this current of philosophy of biology and the scientific ideas around autopoeisis, two independent but parallel developments culminating in the 1970s. Instead of viewing meaning or value as artifacts or illusions, both agree on a new understanding of a form of immanent teleology as truly biological features, inevitably intertwined with the self-establishment of an identity which is the living process. (shrink)

According to the standard view of particularity, an entity is a particular just in case it necessarily has a unique spatial location at any time of its existence. That the basic entities of the world we speak about in common sense and science are particular entities in this sense is the thesis of “foundational particularism,” a theoretical intuition that has guided Western ontological research from its beginnings to the present day. The main aim of this paper is to review the (...) notion of particularity and its role in ontology. I proceed in four steps. First, I offer a brief reconstruction of the tasks of ontology as “theory of categorial inference in L”. An ontological theory states which (combinations of) entity types or categories make true L-sentences true; the features of the stipulated categories explain why L-speakers are entitled to draw certain material inferences from the classificatory expressions of L. Second, I draw attention to the fact that since Aristotle this theoretical program typically has been implemented with peculiar restrictions prescribing certain combinations of category features, e.g., the combination of particularity, concreteness, individuality, and subjecthood. I briefly sketch how these restrictions of the “substance paradigm” or “myth of substance” are reinforced by the standard readings of predicate-logical constants, viz. the existential quantifier and the identity sign. Third, I argue that in the context of the substance paradigm foundational particularism is incoherent. I discuss the current standard conceptions of particulars as developed in the debate about individuation (bare particulars, nude particulars, tropes) and show that their main difficulties derive from the traditional restriction that particulars are so also logical subjects and/or individuals. Fourth, to show that the traditional linkages of category features are not conceptual necessities, I sketch the outlines of an ontology (General Process Theory) based on non-particular individuals. For ontologists in computer science working with description logic this monocategoreal ontology based on more or less generic ‘dynamics’ may hold special interest. As General Process Theory documents, ontologists may well abandon the notion of particularity: in common sense and science we do reason about items that have a unique spatial location at any time, but the uniqueness of their location can be taken to be a contingent affair. (shrink)

The received view in the history of the philosophy of psychology is that the logical positivists—Carnap and Hempel in particular—endorsed the position commonly known as “logical” or “analytical” behaviourism, according to which the relations between psychological statements and the physical-behavioural statements intended to give their meaning are analytic and knowable a priori. This chapter argues that this is sheer legend: most, if not all, such relations were viewed by the logical positivists as synthetic and knowable only a posteriori. It then (...) traces the origins of the legend to the logical positivists’ idiosyncratic extensional or at best weakly intensional use of what are now considered crucially strongly intensional semantic notions, such as “translation,” “meaning” and their cognates, focussing on a particular instance of this latter phenomenon, arguing that a conflation of explicit definition and analyticity may be the chief source of the legend. (shrink)

In this contribution, I comment on Raffaella Campaner’s defense of explanatory pluralism in psychiatry (in this volume). In her paper, Campaner focuses primarily on explanatory pluralism in contrast to explanatory reductionism. Furthermore, she distinguishes between pluralists who consider pluralism to be a temporary state on the one hand and pluralists who consider it to be a persisting state on the other hand. I suggest that it would be helpful to distinguish more than those two versions of pluralism – different understandings (...) of explanatory pluralism both within philosophy of science and psychiatry – namely moderate/temporary pluralism, anything goes pluralism, isolationist pluralism, integrative pluralism and interactive pluralism. Next, I discuss the pros and cons of these different understandings of explanatory pluralism. Finally, I raise the question of how to implement or operationalize explanatory pluralism in scientific practice; how to structure the “genuine dialogue” or shape “the pluralistic attitude” Campaner is referring to. As tentative answers, I explore a question-based framework for explanatory pluralism as well as social-epistemological procedures for interaction among competing approaches and explanations. (shrink)

In the biological realm, a complete explanation of a trait seems to include an explanation in terms of function. It is natural to ask of some trait, "What is its function?" or "What purpose in the organism does the particular trait serve?" or "What is the goal of its activity?" There are several views concerning the appropriate definition of function for biological matters. Two popular views of function with respect to living things are Cummins' organizational account and the Griffiths/Godfrey-Smith modern (...) history account. Whereas Cummins argues that a trait functions so as to contribute to the general organization of some organism's present structure, Griffiths, and Godfrey-Smith argue that a trait functions because of its fitness with respect to the organism's recent evolutionary history. In this paper, I show how these accounts can be made compatible and compliment one another. Given that structure, organization, operational flexibility, function, and evolutionary history are all factors to be considered in an organism's makeup, we should expect that the traits of an organism function the way they do because such traits presently contribute to the overall organization of the organism (Cummins) as well as were selected for in the organism's species' recent ancestry (Griffiths/Godfrey-Smith). (shrink)

Science and engineering rely on the accumulation and dissemination of knowledge to make discoveries and create new designs. Discovery-driven genome research rests on knowledge passed on via gene annotations. In response to the deluge of sequencing big data, standard annotation practice employs automated procedures that rely on majority rules. We argue this hinders progress through the generation and propagation of errors, leading investigators into blind alleys. More subtly, this inductive process discourages the discovery of novelty, which remains essential in biological (...) research and reflects the nature of biology itself. Annotation systems, rather than being repositories of facts, should be tools that support multiple modes of inference. By combining deduction, induction and abduction, investigators can generate hypotheses when accurate knowledge is extracted from model databases. A key stance is to depart from ‘the sequence tells the structure tells the function’ fallacy, placing function first. We illustrate our approach with examples of critical or unexpected pathways, using MicroScope to demonstrate how tools can be implemented following the principles we advocate. We end with a challenge to the reader. (shrink)

In recent years, an increasing number of medical books and papers attempting to analyse the concepts of health and disease from the perspective of evolutionary biology have been published.This paper introduces the evolutionary approach to health and disease in an attempt to illuminate the premisses and the framework of Darwinian medicine. My primary aim is to analyse to what extent evolutionary theory provides for a biological definition of the concept of disease. This analysis reveals some important differences between functional explanations (...) in the field of evolutionary biology and functional explanations in the field of medicine. Moreover, I shall argue that the biological functions relevant to the health of an organism cannot be determined on the basis of evolutionary theory. Accordingly, it seems that Darwinian medicine does not provide for the definition of a biological concept of disease. Still,Darwinian medicine may suggest why we are susceptible to certain diseases; it might also prove a suggestive heuristic on the basis of which new hypotheses concerning relevant treatments of various diseases might be advanced. (shrink)

The design argument was rebutted by David Hume. He argued that the world and its contents (such as organisms) were not analogous to human artifacts. Hume further suggested that there were equally plausible alternatives to design to explain the organized complexity of the cosmos, such as random processes in multiple universes, or that matter could have inherent properties to self-organize, absent any external crafting. William Paley, writing after Hume, argued that the functional complexity of living beings, however, defied naturalistic explanations. (...) In effect he dared anyone to come up with an alternative to his inference to design, and hence a designer, outside of nature. Charles Darwin explained the apparent design of functional complexity by his theory of natural selection. Asa Gray, however, in essays as well as in correspondence with Darwin argued that natural selection allowed for a type of ' evolutionary teleology' in which design at most could be considered the result of universal principles. F. E. Hicks updated Hume by specifically objecting to the use of design arguments by Paley. Hicks argued that the apparent design seen in nature reflected order at a deep level in nature. The design argument was briefly revived by Lawrence Henderson early in the twentieth century but he ultimately concluded that design and teleology were not necessarily mutually entailing and he retracted his design argument in favor of one that he termed ' natural teleology'. The current claims of ' intelligent design' have the same logical problems that have beset previous design arguments. If design is divorced from teleology and its discontents put behind us, then there is a possibility that the latter can have a place in the development of theories to explain the phenomena of emergent complexity. (shrink)

A central aspect of the relation between biosemiotics and biology is investigated by asking: Is a biological concept of function intrinsically related to a biosemiotic concept of sign action, and vice versa? A biological notion of function (as some process or part that serves some purpose in the context of maintenance and reproduction of the whole organism) is discussed in the light of the attempt to provide an understanding of life processes as being of a semiotic nature, i.e., constituted by (...) sign actions. Does signification and communication in biology (e.g., intracellular communication) always presuppose an organism with distinct semiotic or quasi-semiotic functions? And, symmetrically, is it the case that functional relations are simply not conceivable without living sign action? The present note is just an introduction to a project aiming at elucidating the relations between biofunction and biosemiosis. (shrink)

Nietzsche attributes 'will power' to all living things, but this seems in sharp conflict with other positions important to him-and implausible besides. The doctrine smacks of both metaphysics and anthropomorphizing, which he elsewhere derides. Will to power seems to be an intentional end-directedness, involving cognitive or representational powers he is rightly loath to attribute to all organisms, and tends to downplay even in persons. This paper argues that we find a stronger reading of will to power-both more plausible and more (...) consistent with Nietzsche's other views-by developing his affinities with Darwinism. By seeing will to power as an 'internal revision' to Darwinism, opposing the latter's stress (as Nietzsche thinks) on 'survival', but assenting to its uses of natural selection, we can ground or naturalize that notion, congenially to Nietzsche and to us. (shrink)

This paper offers an account of the relationship between inference and explanation in functional morphology which combines Robert Brandon's theory of adaptation explanation with standard accounts of inference to the best explanation. Inferences of function from structure, it is argued, are inferences to the best adaptation explanation. There are, however, three different approaches to the problem of determining which adaptation explanation is the best. The theory of inference to the best adaptation explanation is then applied to a case study from (...) the history of functional morphology: the case of the crested duckbilled dinosaurs. (shrink)