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.

We characterize a type of functional explanation that addresses why a homologous trait originating deep in the evolutionary history of a group remains widespread and largely unchanged across the group’s lineages. We argue that biologists regularly provide this type of explanation when they attribute conserved functions to phenotypic and genetic traits. The concept of conserved function applies broadly to many biological domains, and we illustrate its importance using examples of molecular sequence alignments at the intersection of evolution and cell biology. (...) We use these examples to show how the study of conserved functions can integrate knowledge of a trait’s causal effects on fitness and its history of natural selection without invoking adaptation. We also show how conserved function provides a novel basis for addressing objections against evolutionary functions raised by Robert Cummins. (shrink)

The emerging discipline of evolutionary developmental biology has opened up many new lines of investigation into morphological evolution. Here I explore how two of the core theoretical concepts in ‘evo-devo’ – modularity and homology – apply to evolutionary psychology. I distinguish three sorts of module – developmental, functional and mental modules and argue that mental modules need only be ‘virtual’ functional modules. Evolutionary psychologists have argued that separate mental modules are solutions to separate evolutionary problems. I argue that the structure (...) of developmental modules in an organism helps determine what counts as a separate evolutionary problem for that organism. I suggest that homology as an organizing principle for research in evolutionary psychology, has been severely neglected in favor of analogy (adaptive function). I consider some arguments suggesting that determining homology is less epistemically demanding than determining adaptive function and argue that psychological categories defined by homology are, in fact, more suitable objects of psychological – and particularly neuropsychological – investigation than categories defined by analogy. (shrink)

In this paper, I discuss the question whether objective criteria could be provided for judging something to be a mental illness. I consider the two most prominent objectivist or naturalistic accounts of mental illness, evolutionary and bio-statistical account, which offer such a criterion by relying on the notion of biological function. According to such suggestions, illness is a condition in which there is dysfunciton in some feature of an organism. In this context, I consider different accounts for ascribing functions in (...) biologyand their relationship with the suggested accounts of illnesses. Special focus is placed on the objections according to which the ascription of functions, as envisaged in naturalistic accounts of illness, is incompatible with actual medical and psychiatric practice. I conclude that these objections are legitimate insofar we want to an account of illness that preserves the current practice of ascribing illness. However, the question remains, could a theory that tries to capture the actual medical practice be value-neutral, since our ordinary conception of illness is permeated with value judgments that indirectly enter into medical practice. In that respect, it seems that the requirement for pure objectivity is too strong and thus, it is not reasonable to expect that naturalistic accounts can satisfy it. (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)

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)

Operational definitions of biological altruism in terms of actual fitness exchanges will not work because they include accidental acts as altruistic and exclude altruistic acts that have gone awry. I argue that the definition of biological altruism should contain an analogue of the role intention plays in psychological altruism. I consider two possibilities for this analogue, selected effect functions and the proximate causes and effects of behavior. I argue that the selected-effect function account will not work because it confuses the (...) explanation of some altruistic behavior with the definition of all of it and the information needed to justify a selected effect account of function is too often inaccessible. Close attention to the proximate explanations of a behavior is all that is needed to determine if an act is biologically altruistic, returning biological altruism to descriptive ethology, where it belongs. (shrink)

According to historical theories of biological function, a trait's function is determined by natural selection in the past. I argue that, in addition to historical functions, ahistorical functions ought to be recognized. I propose a theory of biological function which accommodates both. The function of a trait is the way it contributes to fitness and fitness can only be determined relative to a selective regime. Therefore, the function of a trait can only be specified relative to a selective regime. Apart (...) from its desirable pluralism, only this view of relational function can support the function/accident and function/malfunction distinctions commonly thought to be part of the concept of function. Furthermore, only relational function correctly characterizes the explanatory consequences of function attributions in evolutionary biology. (shrink)

There are two general approaches to characterising biological functions. One originates with Cummins. According to this approach, the function of a part of a system is just its causal contribution to some specified activity of the system. Call this the ‘C-function’ concept. The other approach ties the function of a trait to some aspect of its evolutionary significance. Call this the ‘E-function’ concept. According to the latter view, a trait's function is determined by the forces of natural selection. The C-function (...) and E-function concepts are clearly quite different, but there is an important relation between them which heretofore has gone unnoticed. The purpose of this paper is to outline that relation.This is not the first paper to discuss the relation of C-function and E-function. Previous attempts all follow either one of two strategies. The first proposes that the two concepts are ‘unified.’ The other proposes that they are radically distinct and apply to wholly different fields within biology. (shrink)

The most recent resurgence of philosophical attention to the so-called ‘functional talk' in the sciences can be summarized in terms of the following questions: (Q1) What kind of restrictions, and in particular, what kind of evolutionary restrictions as well as to what extent, is involved in functional ascriptions? (Q2) How can we account for the explanatory import of function-ascribing statements? This paper addresses these questions through a modified version of Cummins' functional analysis. The modification in question is concerned with phylogenetical (...) restrictions on causal role functions, and it stems from an analysis of some primary areas in molecular biology. I examine how evolutionary consideration affects the so-called ‘function-analytical explanatory strategy' (Cummins [1975] 1998, 2002). Finally, I argue that the neo-functional analysis here proposed accounts for a certain convergence between the main rival theories of biological function. ‡I wish to thank David Davies, Eva Jablonka, Thomas Reydon, and Marcel Weber for their helpful comments. †To contact the author, please write to: Department of Philosophy, University of Rijeka, Omladinska 14, 51000 Rijeka, Croatia; e-mail: [email protected]. (shrink)

The most recent resurgence of philosophical attention to the so-called ‘functional talk’ in the sciences can be summarized in terms of the following questions: (Q1) What kind of restrictions, and in particular, what kind of evolutionary restrictions as well as to what extent, are involved in functional ascriptions? (Q2) How can we account for the explanatory import of function-ascribing statements? This paper addresses these questions on the basis of a modified version of Cummins’ functional analysis. The modification in question is (...) concerned with phylogenetical restrictions on causal role functions, and it stems from an analysis of some primary areas in molecular biology. I examine how evolutionary consideration affects the so-called “function-analytical explanatory strategy” (Cummins [1975] 1998, 2002). Finally, I argue that the neo-functional analysis here proposed accounts for a certain convergence between the main rival theories of biological function. (shrink)

What are the prospects for a monistic view of biological individuality given the multiple epistemic roles the concept must satisfy? In this paper, I examine the epistemic adequacy of two recent accounts based on the capacity to undergo natural selection. One is from Ellen Clarke, and the other is by Peter Godfrey-Smith. Clarke’s position reflects a strong monism, in that she aims to characterize individuality in purely functional terms and refrains from privileging any specific material properties as important in their (...) own right. I argue that Clarke’s functionalism impairs the epistemic adequacy of her account compared to a middle-ground position taken by Godfrey-Smith. In comparing Clarke and Godfrey-Smith’s account, two pathways emerge to pluralism about biological individuality. The first develops from the contrast between functionalist and materialist approaches, and the second from an underlying temporal structure involved in using evolutionary processes to define individuality. (shrink)

We introduce a new type of pluralism about biological function that, in contrast to existing, demonstrates a practical integration among the term’s different meanings. In particular, we show how to generalize Sandra Mitchell’s notion of integrative pluralism to circumstances where multiple epistemic tools of the same type are jointly necessary to solve scientific problems. We argue that the multiple definitions of biological function operate jointly in this way based on how biologists explain the evolution of protein function. To clarify how (...) our account relates to existing views, we introduce a general typology for monist and pluralist accounts along with standardized criteria for judging which is best supported by evidence. (shrink)

The notion of function is indispensable to our understanding of distinctions such as that between being broken and being in working order (for artifacts) and between being diseased and being healthy (for organisms). A clear account of the ontology of functions and functioning is thus an important desideratum for any top-level ontology intended for application to domains such as engineering or medicine. The benefit of using top-level ontologies in applied ontology can only be realized when each of the categories identified (...) and defined by a top-level ontology is integrated with the others in a coherent fashion. Basic Formal Ontology (BFO) has from the beginning included function as one of its categories, exploiting a version of the etiological account of function that is framed at a level of generality sufficient to accommodate both biological and artifactual functions. This account has been subjected to a series of criticisms and refinements. We here articulate BFO’s account of function, provide some reasons for favoring it over competing views, and defend it against objections. (shrink)

Many people argue that history makes a special difference to the subjects of biology and psychology, and that history does not make this special difference to other parts of the world. This paper will show that historical properties make no more or less of a difference to biology or psychology than to chemistry, physics, or other sciences. Although historical properties indeed make a certain kind of difference to biology and psychology, this paper will show that historical properties make the same (...) kind of difference to geology, sociology, astronomy, and other sciences. Similarly, many people argue that nonhistorical properties make a special difference to the nonbiological and the nonpsychological world. This paper will show that nonhistorical properties make the same difference to all things in the world when it comes to their causal behavior and that historical properties make the same difference to all things in the world when it comes to their distributions. Although history is special, it is special in the same way to all parts of the world. (shrink)

Different chemical species are often cited as paradigm examples of structurally delimited natural kinds. While classificatory monism may thus seem plausible for simple molecules, it looks less attractive for complex biological macromolecules. I focus on the case of proteins that are most plausibly individuated by their functions. Is there a single, objective count of proteins? I argue that the vagaries of function individuation infect protein classification. We should be pluralists about macromolecular classification.

"Modern History" versions of the etiological theory claim that in order for a trait X to have the proper function F, individuals with X must have been recently favored by natural selection for doing F (Godfrey-Smith 1994; Griffiths 1992, 1993). For many traits with prototypical proper functions, however, such recent selection may not have occurred: traits may have been maintained due to lack of variation or due to selection for other effects. I examine this flaw in Modern History accounts and (...) offer an alternative etiological theory, the Continuing Usefulness account, which appears to avoid such problems. (shrink)

There is a conceptual crisis in the biomedical sciences that is particularly salient in psychopathology research. Underlying the crisis is a controversy that pertains to the current medical model of disease that largely draws from causal-mechanistic explanations. The bedrock of this model is the analysis of biological part-dysfunctions that aims at unequivocally defining a pathological condition and demarcating it from its neighboring entities. This endeavor has led to a quest for physiological, biochemical, and genetic signatures. Yet, so far there is (...) little evidence for reliable biomarkers for any mental disorder. The contemporary biomedical paradigm largely ignores historical, dynamic, and system-level aspects—a view that has contributed much to the conceptual disjunction of the patient as a person from his/her disease. Notwithstanding the impressive progress in the biomedical sciences, increasingly more critics question whether the constituting framework is sufficient to convey a comprehensive understanding of illnesses, especially mental illnesses. Thus, the medical model urgently requires an update. But rather than revamping it by methodological advancements, it will be necessary to critically review its philosophical roots. The most problematic issues that require reworking are: the preponderance of the biostatistical theory; the undue decoupling of physiological from evolutionary explanations of function; the clinging to the Modern Synthesis ; and the neglect of dynamic and system-level properties. The proposed overhaul requires the heeding of historical explanations that draw from the Extended Evolutionary Synthesis as well as systems biology approaches for tackling multilevel and dynamic phenomena of complex systems. (shrink)

There is a conceptual crisis in the biomedical sciences that is particularly salient in psychopathology research. Underlying the crisis is a controversy that pertains to the current medical model of disease that largely draws from causal-mechanistic explanations. The bedrock of this model is the analysis of biological part-dysfunctions that aims at unequivocally defining a pathological condition and demarcating it from its neighboring entities. This endeavor has led to a quest for physiological, biochemical, and genetic signatures. Yet, so far there is (...) little evidence for reliable biomarkers for any mental disorder. The contemporary biomedical paradigm largely ignores historical, dynamic, and system-level aspects—a view that has contributed much to the conceptual disjunction of the patient as a person from his/her disease. Notwithstanding the impressive progress in the biomedical sciences, increasingly more critics question whether the constituting framework is sufficient to convey a comprehensive understanding of illnesses, especially mental illnesses. Thus, the medical model urgently requires an update. But rather than revamping it by methodological advancements, it will be necessary to critically review its philosophical roots. The most problematic issues that require reworking are: the preponderance of the biostatistical theory; the undue decoupling of physiological from evolutionary explanations of function; the clinging to the Modern Synthesis ; and the neglect of dynamic and system-level properties. The proposed overhaul requires the heeding of historical explanations that draw from the Extended Evolutionary Synthesis as well as systems biology approaches for tackling multilevel and dynamic phenomena of complex systems. (shrink)

Editors' introduction to the special issue on homology (Biology and Philosophy Vol. 22, Issue 5, 2007).

Contemporary analyses of biological function almost invariably advocate a naturalistic analysis, grounding biological functions in some feature of the mind-independent world. Many recent accounts suggest that no single analysis will be appropriate for all cases of use and that biological teleology should be split into several distinct categories. This paper argues that such accounts have paid too little attention to the way in which functional language is used, concentrating instead on the types of situation in which it is used. An (...) example of the role of teleology in science is examined and, on the basis of conclusions drawn from this, an alternative unifying analysis is proposed. It is suggested that, contrary to naturalistic accounts, teleology in biology carries no ontological commitment whatsoever to any class of mind-independent entities or properties. Instead, it is best regarded as a methodological device which is used to focus interest, formulate research perspectives and facilitate the structuring of certain questions or types of question that are pertinent in a given context of interest. (shrink)

In this paper, I consider V. S. Ramachandran's in-principle agnosticism concerning whether neurological studies of religious experience can be taken as support for the claim that God really does communicate with people during religious experiences. Contra Ramachandran, I argue that it is by no means obvious that agnosticism is the proper scientific attitude to adopt in relation to this claim. I go on to show how the questions of whether it is (1) a scientifically testable claim and (2) a plausible (...) hypothesis, serve to open up some important philosophical issues concerning interpretive backgrounds that are presupposed in the assessment of scientific hypotheses. More specifically, I argue that naturalism or scientific objectivism in its various forms is not simply a neutral or default methodological backdrop for empirical inquiry but involves acceptance of a specific ontology, which functions as an implicit and unargued constitutive commitment. Hence, these neurological studies can be employed as a lever with which to disclose something of the ways in which different frameworks of interpretation, both theistic and atheistic, serve differently to structure and give meaning to empirical findings. (shrink)

I examine the way in which Daniel Dennett (1987, 1995) uses his 'intentional' and 'design' stances to make the claim that intentionality is derived from design. I suggest that Dennett is best understood as attempting to supply an objective, nonintentional, naturalistic rationale for our use of intentional concepts. However, I demonstrate that his overall picture presupposes prior application of the intentional stance in a preconditional, ineliminable,'sense-giving' role. Construed as such, Dennett's account is almost identical to the account of biological teleology (...) offered by Kant in The Critique of Judgement, with the consequence that Dennett's naturalism is untenable. My conclusions lead to doubts concerning the legitimacy of any account attempting to naturalise intentionality by extracting normativity from biology and also point to a novel account of biological function. (shrink)

The notion of biological function is fraught with difficulties—intrinsically and irremediably so, we argue. The physiological practice of functional ascription originates from a time when organisms were thought to be designed and remained largely unchanged since. In a secularized worldview, this creates a paradox which accounts of functions as selected effect attempt to resolve. This attempt, we argue, misses its target in physiology and it brings problems of its own. Instead, we propose that a better solution to the conundrum of (...) biological functions is to abandon the notion altogether, a prospect not only less daunting than it appears, but arguably the natural continuation of the naturalisation of biology. (shrink)

This article draws out an epistemological tension implicit in Cosmides and Tooby's conception of evolutionary psychology. Cosmides and Tooby think of the mind as a collection of functionally individuated, domain-specific modules. Although they do not explicitly deny the existence of domain-general processes, it will be shown that their methodology commits them to the assumption that only domain-specific cognitive processes are capable of producing useful outputs. The resultant view limits the scope of biologically possible cognitive accomplishments and these limitations, it will (...) be argued, are such as to deny us epistemic capacities that evolutionary psychology presupposes in its pursuit of an objective, comprehensive account of human nature. (shrink)

On dit souvent que, tandis que la biologie de l'évolution utilise un concept étiologique de fonction (la fonction d'un trait biologique n'est autre que son effet sélectionné), la physiologie prend appui sur un autre concept de fonction, celui de rôle causal. Cependant, un examen plus attentif montre que le concept non normatif de rôle causal n'est pas ce dont la physiologie générale ou la neurophysiologie ont besoin. Ces disciplines font un large usage de notions comme celles de bon fonctionnement, de (...) fonctionnement normal, de fonctionnement perturbé ou de trouble fonctionnel. Il semble ainsi qu'un concept normatif comme le concept étiologique n'est pas seulement utile dans le contexte d'explications téléologiques ou évolutionnistes, mais aussi dans celui d'explications mécanistes ou opérationnelles telles qu'elles sont couramment proposées par la physiologie. La différence entre types d'explication n'est pas une différence entre deux concepts de fonction. En particulier, l'analyse physiologique serait une tâche impossible si elle devait prendre en compte toutes les relations causales à l'intérieur de l'organisation fonctionnelle de chaque système biologique. Pour résoudre ce problème, la physiologie doit être une analyse du fonctionnement normal du système, quelle que soit la part d'idéalisation nécessaire. La notion de bon fonctionnement, conçu comme le produit de l'histoire évolutive, nous aide en particulier à comprendre pourquoi les systèmes qui fonctionnent bien se ressemblent, et pourquoi les systèmes qui dysfonctionnent peuvent le faire de tant de façons différentes. It is often claimed that although evolutionary biology uses an etiological concept of function (according to etiological theory, the function of a biological feature is its selected effect), physiology relies on a different concept of function, the causal role concept. However, upon closer scrutiny, it appears that the non-normative causal role concept is not what is needed by physiology or neurophysiology. These disciplines make a wide use of normative notions like proper functioning, normal functioning, impaired functioning, or functional disorders. In this case, it seems that a normative concept like the etiological concept is not only useful in the context of teleological or evolutionary explanations, but also in the context of mechanical or operational explanations as they are routinely offered by physiology. The difference between types of explanations is not a difference between two kinds of concepts of function. In particular, physiological analysis would be an impossible task if it had to take into account all causal links within the functional organization of each biological system. To solve this problem, physiology has to be the analysis of the proper or normal functioning of the system, even if normal functioning is usually obtained through a process of idealization. The notion of proper functioning, conceived as the product of evolutionary history, helps us understand, among other things, why properly functioning systems tend to be similar, and why malfunctioning systems may differ in so many different ways. (shrink)

This paper argues that a minimal notion of function and a notion of normal-proper function are used in explaining how bodies and brains operate. Neither is Cummins’ notion, as originally defined, and yet his is often taken to be the clearly relevant notion for such an explanatory context. This paper also explains how adverting to normal-proper functions, even if these are selected functions, can play a significant scientific role in the operational explanations of complex systems that physiologists and neurophysiologists provide, (...) despite a lack of relevant causal efficacy on the part of such functions. (shrink)

There are two very different ways of thinking about perception. According to representationalism, perceptual states are representations: they represent the world as being a certain way. They have content, which may or may not be different from the content of beliefs. They represent objects as having properties, sometimes veridically, sometimes not. According to relationalism, perception is a relation between the agent and the perceived object. Perceived objects are literally constituents of our perceptual states and not of the contents thereof. Perceptual (...) states are not representations. My aim is to argue that if we frame this debate as a debate about the individuation of perceptual states, rather than the nature of perception, then we can reconcile these two seemingly conflicting ways of thinking about perception. (shrink)

One of the most influential arguments against the claim that computers can think is that while our intentionality is intrinsic, that of computers is derived: it is parasitic on the intentionality of the programmer who designed the computer-program. Daniel Dennett chose a surprising strategy for arguing against this asymmetry: instead of denying that the intentionality of computers is derived, he endeavours to argue that human intentionality is derived too. I intend to examine that biological plausibility of Dennett’s suggestion and show (...) that Dennett’s argument for the claim that human intentionality is derived because it was designed by natural selection is based on the misunderstanding of how natural selection works. (shrink)

The functional complexity, or the number of functions, of organisms hasfigured prominently in certain theoretical and empirical work inevolutionary biology. Large-scale trends in functional complexity andcorrelations between functional complexity and other variables, such assize, have been proposed. However, the notion of number of functions hasalso been operationally intractable, in that no method has been developedfor counting functions in an organism in a systematic and reliable way.Thus, studies have had to rely on the largely unsupported assumption thatnumber of functions can be (...) measured indirectly, by using number ofmorphological, physiological, and behavioral parts as a proxy. Here, amodel is developed that supports this assumption. Specifically, the modelpredicts that few parts will have many functions overlapping in them, andtherefore the variance in number of functions per part will be low. If so,then number of parts is expected to be well correlated with number offunctions, and we can use part counts as proxies for function counts incomparative studies of organisms, even when part counts are low. Alsodiscussed briefly is a strategy for identifying certain kinds of parts inorganisms in a systematic way. (shrink)

The specialization of visual function within biological function is reason for introducing “homology thinking” into explanations of the visual system. It is argued that such specialization arises when organisms evolve by differentiation from their predecessors. Thus, it is essentially historical, and visual function should be regarded as a lineage property. The colour vision of birds and mammals do not function the same way as one another, on this account, because each is an adaptation to special needs of the visual functions (...) of predecessors—very different kinds of predecessors in each case. Thus, history underlies function. We also see how homology thinking figures in the hierarchical classification of visual systems, and how it supports the explanation of visual function by functional role analysis. (shrink)

It is widely assumed that selection history accounts of function can support a fully reductive naturalization of functional properties. I argue that this assumption is false. A problem with the alternative causal role account of function in this context is that it invokes the teleological notion of a goal in analysing real function. The selection history account, if it is to have reductive status, must not do the same. But attention to certain cases of selection history in biology, specifically those (...) involving meiotic drive, shows that selection historical explanations are available in the case of items without any plausible function. Making contributions to goals, here fitness, must be introduced as an additional constraint in the analysis, either explicitly, or implicitly by appeal to individual functions or the selection-of/selection-for distinction. (shrink)

Normative standards are often applied to emotions. Are there normative standards that apply to emotions in virtue solely of facts about their nature? I will argue that the answer is no. The psychological, behavioural, and neurological evidence suggests that emotions are representational brain states with various kinds of biological functions. Facts about biological functions are not (and do not by themselves entail) normative facts. Hence, there are no nor- mative standards that apply to emotions just in virtue of their having (...) various kinds of biolog- ical functions. Moreover, the peculiar features of emotions make the view that representational content is essentially normative very implausible. Hence, the representational properties of emotions cannot be seen as entailing normative standards. The conclusion is that there are no normative standards that apply to emotions solely in virtue of their nature. Ó 2005 Elsevier Ltd. All rights reserved. (shrink)

In this paper we examine the following problems: How many concepts of function are there in biology, social science, and technology? Are they logically related and if so, how? Which of these function concepts effect a functional explanation as opposed to a mere functional account? What are the consequences of a pluralist view of functions for functionalism? We submit that there are five concepts of function in biology, which are logically related in a particular way, and six function concepts in (...) social science and technology. Only two of them may help effect a genuine functional explanation. Finally, our synthetic approach allows us to distinguish four different varieties of functionalism in biology, psychology, social science, and technology: formalist, black boxist, adaptationist, and teleological. And only one of them is explanatory in the strong sense defended here. (shrink)

Evolutionary psychology tends to be associated with a massively modular cognitive architecture. On this framework of human cognition, an assembly of specialized information processors called modules developed under selection pressures encountered throughout the phylogenic history of hominids. The coordinated activity of domain-specific modules carries out all the processes of belief fixation, abstract reasoning, and other facets of central cognition. Against the massive modularity thesis, I defend an account of systemic functional adaptedness, according to which non-modular systems emerged because of adaptive (...) problems imposed by the intrinsic physiology of the evolving human brain. The proposed reformulation of evolutionary theorizing draws from neural network models and Cummins’ (1975) account of systemic functions to identify selection pressures that gave rise to non-modular, domain-general mechanisms in cognitive architecture. (shrink)

Evolutionary developmental biology (Evo-devo) is a vibrant area of contemporary life science that should be (and is) increasingly incorporated into teaching curricula. Although the inclusion of this content is important for biological pedagogy at multiple levels of instruction, there are also philosophical lessons that can be drawn from the scientific practices found in Evo-devo. One feature of particular significance is the interdisciplinary nature of Evo-devo investigations and their resulting explanations. Instead of a single disciplinary approach being the most explanatory or (...) fundamental, different methodologies from biological disciplines must be synthesized to generate empirically adequate explanations. Thus, Evo-devo points toward a non-reductionist epistemology in biology. I review three areas where these synthetic efforts become manifest as a result of Evo-devo’s practices (form versus function reasoning styles; problem-structured investigations; idealizations related to studying model organisms), and then sketch some possible applications to teaching biology. These philosophical considerations provide resources for life science educators to address (and challenge) key aspects of the National Science Education Standards and Benchmarks for Scientific Literacy. (shrink)

“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)

The distinction between causal role and selected effect functions is typically framed in terms of their respective explanatory roles. However, much of the controversy over functions in genomics takes place in an investigative, not an explanatory context. Specifically, the process of component-driven functional investigation begins with the designation of some genetic or epigenetic element as functional —i.e. not junk— because it possesses properties that, arguably, suggest some biologically interesting organismal effect. The investigative process then proceeds, in a bottom-up fashion, to (...) search for those effects. I argue that this process encounters a problem reminiscent of one that Gould and Lewontin associated with the adaptationist program. Just as their stereotypical adaptationst became trapped in the myopic pursuit of one selectionist hypothesis after another, so can the investigation of CR functions in genomics lead to an unending series putative organism-level CR functions for junk DNA. This is an acute problem for genomics, because eukaryotic genomes are littered with transposable elements and their deactivated descendants which often masquerade as interesting CR-functional components and it is experimentally onerous to determine whether they lack such a function. I further argue that selectionist reasoning about TE-host coevolutionary dynamics can greatly streamline the investigative process. Importantly, selectionist hypotheses need not be well confirmed to be illuminating in this context. Informed selectionist reasoning about the strategic roles of TEs in the genome offers a corrective to the idea that most of our DNA is somehow CR functional for the organism. (shrink)

The rights and wrongs of adaptationism areoften discussed by appeal to what I call theartefact model. Anti-adaptationistscomplain that the use of optimality modelling,reverse engineering and other techniques areindicative of a mistaken and outmoded beliefthat organisms are like well-designedartefacts. Adaptationists (e.g. Dennett 1995)respond with the assertion that viewingorganisms as though they were well designed isa fruitful, perhaps necessary research strategyin evolutionary biology. Anti-adaptationistsare right when they say that techniques likereverse engineering are liable to mislead. This fact does not undermine the artefact (...) modelprecisely because the same techniques misleadus for the same reasons when they are appliedunreflectively to artefacts. Thoseadaptationists who hold only that it isworthwhile to investigate organisms as thoughthey were artefacts and thoseanti-adaptationists who criticise simplisticdesign models have far more in common than thelabels attached to their positions mightsuggest. (shrink)

If ecological systems are functionally organised, they can possess functions or malfunctions. Natural function would provide justification for conservationists to act for the protection of current ecological arrangements and control the presence of populations that create ecosystem malfunctions. Invasive species are often thought to be malfunctional for ecosystems, so functional arrangement would provide an objective reason for their control. Unfortunately for this prospect, I argue no theory of function, which can support such normative conclusions, can be applied to large scale (...) ecosystems. Instead ecological systems have causal structure, with small clusters of populations achieving functional arrangement. This, however, does not leave us without reason to control invasive species. We can look at the causal arrangement of ecological systems for populations that support ecological features that we should preserve. Populations that play a causal role in reducing biodiversity should be controlled, because biodiversity is a good all prudent agents should want to preserve. (shrink)

If ecological systems are functionally organised, they can possess functions or malfunctions. Natural function would provide justification for conservationists to act for the protection of current ecological arrangements and control the presence of populations that create ecosystem malfunctions. Invasive species are often thought to be malfunctional for ecosystems, so functional arrangement would provide an objective reason for their control. Unfortunately for this prospect, I argue no theory of function, which can support such normative conclusions, can be applied to large scale (...) ecosystems. Instead ecological systems have causal structure, with small clusters of populations achieving functional arrangement. This, however, does not leave us without reason to control invasive species. We can look at the causal arrangement of ecological systems for populations that support ecological features that we should preserve. Populations that play a causal role in reducing biodiversity should be controlled, because biodiversity is a good all prudent agents should want to preserve. (shrink)

Philosophical analyses of scientific concepts are legion. However, this literature is replete with methodological errors that have largely gone unnoticed. Five distinct projects are conflated which has led to faulty inferences, ambiguities, and mischaracterizations. There has also been some recent enthusiasm for approaches that attempt to rectify problematic scientific concepts but the motivations for these approaches are questionable. I am hopeful that by bringing these various issues to light that it will lead practitioners to be more explicit about their aims (...) and subsequently result in better analyses. (shrink)