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 MPhil dissertation presents a novel account of teleological explanations in biology. I outline the “shorthand approach” to such explanations, on which they are taken to convey implicit evolutionary explanations. “Selected effects” accounts of teleological explanation dominate recent literature, but they struggle to accommodate teleological explanations of complex traits built through cumulative selection. I articulate the general notion of a landscape explanation, which, applied to biology, explains the evolution of complex features in a population by citing salient features of the (...) population’s fitness landscape. I show that such explanations lend themselves to a teleological shorthand. I close with remarks concerning when a teleological explanation of a trait is legitimate, and why teleological language strikes us as appropriate when we give evolutionary explanations. (shrink)

A distinction between different notions of “structure” and “function” is suggested for interpreting the overwhelming amount of data on microbiome structure and function. Sequence data, biochemical agents, interaction networks, taxonomic communities, and their dynamics can be linked to potential or actual biochemical activities, causal roles, and selected effects, respectively. This conceptual clarification has important methodological consequences for how to interpret existing data and approach open questions in contemporary microbiome research practice. In particular, the field will have to start thinking about (...) notions of function more directly. Also see the video abstract here https://youtu.be/j5pq5uGld1k. (shrink)

Various prominent theories of pain assume that it is pain’s biological function to inform organisms about damage to their bodies. I argue that this is a mistake. First, there is no biological evidence to support the notion that pain was originally selected for its informative capacities, nor that it currently contributes to the fitness of organisms in this specific capacity. Second, neurological evidence indicates that modulating mechanisms in the nociceptive system systematically prevent pain from serving a primarily informative role. These (...) considerations threaten to undermine standard perceptual and representational accounts of pain. (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)

It is widely assumed that functional and dispositional properties are not identical to their physical base, but that there is some kind of asymmetrical ontological dependence between them. In this regard, a popular idea is that the former are realized by the latter, which, under the non-identity assumption, is generally understood to be a non-causal, constitutive relation. In this paper we examine two of the most widely accepted approaches to realization, the so-called ‘flat view’ and the ‘dimensioned view’, and we (...) analyze their explanatory relevance in the light of a number of examples from the life sciences, paying special attention to developmental phenomena. Our conclusion is that the emphasis placed by modern-day biology on such properties as variability, evolvability, and a whole collection of phenomena like modularity, robustness, and developmental constraint or developmental bias requires the adoption of a much more dynamic perspective than traditional realization frameworks are able to capture. (shrink)

John Searle has argued that functions owe their existence to the value that we put into life and survival. In this paper, I will provide a critique of Searle’s argument concerning the ontology of functions. I rely on a standard analysis of functional predicates as relating not only a biological entity, an activity that constitutes the function of this entity and a type of system but also a goal state. A functional attribution without specification of such a goal state has (...) no truth-value. But if completed with a goal state, functional attributions understood as four-place relations attain a truth-value. The truth conditions of all attributions of function involve a dependence claim of the goal state on the function bearer’s activity. The nature of this dependence may differ; I consider five different possibilities: causality, mechanistic constitution, mereology, supervenience and metaphysical grounding. If these dependency relations are objective, Searle’s central ontological thesis fails. What he ought to have said is that our valuing survival or other goal states may be the reason why biology seeks functional knowledge, but this has nothing to do with ontology. I will show further that Searle also raised an interesting challenge concerning the relationship of functional and causal truths, but it does not threaten the objectivity of functions either. At best, it could show that functional vocabulary is eliminable. However, I will show that functional vocabulary is not so eliminable. (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.

Defenders of evolutionary medicine claim that medical professionals and public health officials would do well to consider the role of evolutionary biology with respect to the teaching, research, and judgments pertaining to medical theory and practice. An integral part of their argument is that the human body should be understood as a bundle of evolutionary compromises. Such an appreciation, which includes a proper understanding of biological function and physiological homeostasis, would provide a crucial perspective regarding the understanding and securing of (...) human health needs currently lacking in the medical arena. (shrink)

This special issue of Applied Ontology is devoted to the foundation, the comparison and the application of functional theories in all areas, with particular attention to the biological and engineering domains. It includes theoretical and technical contributions related to the description, characterization, and application of functions.

A common misunderstanding of the selected effects theory of function is that natural selection operating over an evolutionary time scale is the only functionbestowing process in the natural world. This construal of the selected effects theory conflicts with the existence and ubiquity of neurobiological functions that are evolutionary novel, such as structures underlying reading ability. This conflict has suggested to some that, while the selected effects theory may be relevant to some areas of evolutionary biology, its relevance to neuroscience is (...) marginal. This line of reasoning, however, neglects the fact that synapses, entire neurons, and potentially groups of neurons can undergo a type of selection analogous to natural selection operating over an evolutionary time scale. In the following, I argue that neural selection should be construed, by the selected effect theorist, as a distinct type of function-bestowing process in addition to natural selection. After explicating a generalized selected effects theory of function and distinguishing it from similar attempts to extend the selected effects theory, I do four things. First, I show how it allows one to identify neural selection as a distinct function-bestowing process, in contrast to other forms of neural structure formation such as neural construction. Second, I defend the view from one major criticism, and in so doing I clarify the content of the view. Third, I examine drug addiction to show the potential relevance of neural selection to neuroscientific and psychological research. Finally, I endorse a modest pluralism of function concepts within biology. (shrink)

This paper presents a way of classifying different forms of naturalness and unnaturalness. Three main forms of (un)naturalness are found as the following: history- based (un)naturalness, property-based (un)naturalness and relation-based (un)naturalness. Numerous subforms (and some subforms of the subforms) of each are presented. The subforms differ with respect to the entities that are found (un)natural, with respect to their all-inclusiveness, and whether (un)naturalness is seen as all-or-nothing affair, or a continuous gradient. This kind of conceptual analysis is needed, first, because (...) discussion concerning (un)naturalness is common in current bioethics and environmental ethics, and second, because the terms natural and unnatural are highly ambiguous. Thus, the lack of an exact definition of the type of (un)naturalness may lead into equivocation, other forms of bad argumentation, or at least vagueness. (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)

The present thesis explores some metaphysical issues concerning biochemical kinds and the relations between chemical and biological properties and phenomena. The main result of this thesis is that there is something sui generis about biochemical kinds. This result is motivated by two theoretical steps. The first is characterising biochemical functions as weakly emergent from the chemical structure [Chapter 3, Chapter 6]. The second is via an account for which biochemical kinds are natural categories [Chapter 4, Chapter 7]. The thesis comprises (...) four parts. Part I [Chapter 1, Chapter 2] aims to offer the methodological and conceptual tools that underpin this research. Chapter 1 presents the debate on the unity of science and the motivation of the research. Chapter 2 presents the account of natural kinds that will be used throughout the thesis. Part II [Chapter 3, Chapter 4] offers a detailed metaphysical analysis of the molecular gene. Chapter 3 argues that molecular genes are weakly emergent from nucleic acids. Chapter 4 argues that the category "molecular gene" can be deemed a natural kind, following the account presented in Chapter 2. Part III [Chapter 5, Chapter 6, Chapter 7] explores some of the themes related to biochemical kinds and generalises some of the results from Part II. Chapter 5 considers biochemical functions and how functional attribution should be interpreted for biochemical molecules. Chapter 6 considers the relation between biochemical functions and structure, spelt in terms of weak emergence and explores unity in biochemistry. Chapter 7 considers the topic of biochemical kinds per se and argues that biochemical kinds are natural categories. Part IV [Chapter 8] elucidates the main outcome and the implications that this research can have for future discussion in the philosophy and metaphysics of biochemistry and the unity of science. (shrink)

There have been repeated attempts in the history of comparative biology to provide a mechanistic account of morphological homology. However, it is well-established that homologues can develop from diverse sets of developmental causes, appearing not to share any core causal architecture that underwrites character identity. We address this challenge with a new conceptual model of Character Identity Mechanisms. ChIMs are cohesive mechanisms with a recognizable causal profile that allows them to be traced through evolution as homologues despite having a diverse (...) etiological organization. Our model hypothesizes that anatomical units at different levels of organization—cell types, tissues, and organs—have level-specific ChIMs with different conserved parts, activities, and organization. Relying on a methodology of conceptual engineering, we show how the ChIM concept advances our understanding of the developmental basis of morphological characters, while forging an important link between comparative and mechanistic biology. (shrink)

In the recent literature on explanation in biology, increasing attention is being paid to the connection between design explanation and mechanistic explanation, viz. the role of design principles and heuristics for mechanism discovery and mechanistic explanation. In this paper we extend the connection between design explanation and mechanism discovery by prizing apart two different types of design explanation and by elaborating novel heuristics that one specific type offers for mechanism discovery across species. We illustrate our claims in terms of two (...) lines of biological research on the biological advantages of organismal traits, one on the eye-size of giant squid, the other on foraging habits of specific bat species. We argue that this research illustrates useful heuristics for mechanism discovery across species, viz. reasoning strategies to infer likely mechanisms for a certain biological role based on assessments of the environmental conditions in which the role is performed efficiently and less or in-efficiently. We bring out the novel features of our analysis in terms of a comparison with mechanistic approaches to mechanism discovery, amongst which graph-theoretical ones, and by comparing the different types of design explanation and the discovery heuristics they support. (shrink)

Scientists, philosophers, and even the lay public commonly accept that schizophrenia stems from a biological or internal ‘dysfunction.’ However, this assessment is typically accompanied neither by well-defined criteria for determining that something is dysfunctional nor empirical evidence that schizophrenia satisfies those criteria. In the following, a concept of biological function is developed and applied to a neurobiological model of schizophrenia. It concludes that current evidence does not warrant the claim that schizophrenia stems from a biological dysfunction, and, in fact, that (...) unusual neural structures associated with schizophrenia may have functional or adaptive significance. The fact that current evidence is ambivalent between these two possibilities (dysfunction versus adaptive function) implies that schizophrenia researchers should be much more cautious in using the ‘dysfunction’ label than they currently are. This has implications for both psychiatric treatment as well as public perception of mental disorders. (shrink)

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

This article offers an analysis of ecologist Charles Elton’s “functional” concept of the niche and of the notion of function implicitly associated with it. It does so in part by situating Elton’s niche concept within the broader context of the “functionalist-interactionist” approach to ecology he introduced, and in relation to his views on the relationship between ecology and evolution. This involves criticizing the common claim that Elton’s idea of species as fulfilling functional roles within ecological communities committed him to an (...) idea of communities as units of selection. While such a claim implicitly attributes to Elton an understanding of function along the lines of the selected-effects theory of function advocated by many biologists and philosophers of biology, Elton’s use of the niche concept, I maintain, involves an understanding of function more along the lines of alternative nonselectionist theories such as the causal-role, goal-contribution, and organizational theories. I also briefly discuss how ecologists after Elton also tend to have typically adopted a nonselectionist understanding of the function concept, similar to his. (shrink)

After describing the disorder of psychopathy, I examine the theories and the evidence concerning the psychopaths’ deficient moral capacities. I first examine whether or not psychopaths can pass tests of moral knowledge. Most of the evidence suggests that they can. If there is a lack of moral understanding, then it has to be due to an incapacity that affects not their declarative knowledge of moral norms, but their deeper understanding of them. I then examine two suggestions: it is their deficient (...) practical reason or their stunted emotions that are at fault. The evidence supports both explanations. I conclude with an overview of the debate concerning whether they are morally or legally responsible for their actions. (shrink)

I distinguish two forms of pluralism about biological functions, between-discipline pluralism and within-discipline pluralism. Between-discipline pluralism holds that different theories of function are appropriate for different subdisciplines of biology and psychology. I provide reasons for rejecting this view. Instead, I recommend within-discipline pluralism, which emphasizes the plurality of function concepts at play within any given subdiscipline of biology and psychology.

Many argue that higher-cognitive emotions such as pride arose de novo in humans, and thus fall outside of the scope of the kinds of evolutionary explanations offered for ?basic emotions,? like fear. This approach fractures the general category of ?emotion? into two deeply distinct kinds of emotion. However, an increasing number of emotion researchers are converging on the conclusion that higher-cognitive emotions are evolutionarily rooted in simpler emotional responses found in primates. I argue that pride fits this pattern, and then (...) consider some of the possible mechanisms by which the basic forms of these emotions have been transformed, arguing that we can see this transformation in part as the progressive internalization of originally externalized processes associated with norms, selfhood, and social structure. This connects the emotion literature with the literatures on the Social/Machiavellian Intelligence Hypothesis and situated cognition, offering the possibility of a more unified theory of human emotions. (shrink)

The philosophy of science that grew out of logical positivism construed scientific knowledge in terms of set of interconnected beliefs about the world, such as theories and observation statements. Nowadays science is also conceived of as a dynamic process based on the various practices of individual scientists and the institutional settings of science. Two features particularly influence the dynamics of scientific knowledge: epistemic standards and aims (e.g., assumptions about what issues are currently in need of scientific study and explanation). While (...) scientific beliefs are representations of the world, scientific standards and aims are epistemic values. The relevance of epistemic aims and values for belief change has been previously recognized. My paper makes a similar point for scientific concepts, both by studying how an individual concept changes (in its semantic properties) and by viewing epistemic aims and values tied to individual concepts. (shrink)

Despite the voluminous literature on biological functions produced over the last 40 years, few philosophers have studied the concept of function as it is used in neuroscience. Recently, Craver (forthcoming; also see Craver 2001) defended the causal role theory against the selected effects theory as the most appropriate theory of function for neuroscience. The following argues that though neuroscientists do study causal role functions, the scope of that theory is not as universal as claimed. Despite the strong prima facie superiority (...) of the causal role theory, the selected effects theory (when properly developed) can handle many cases from neuroscience with equal facility. It argues this by presenting a new theory of function that generalizes the notion of a ‘selection process’ to include processes such as neural selection, antibody selection, and some forms of learning—that is, to include structures that have been differentially retained as well as those that have been differentially reproduced. This view, called the generalized selected effects theory of function, will be defended from criticism and distinguished from similar views in the literature. (shrink)

Dobzhansky argued that biology only makes sense if life on earth has a shared history. But his dictum is often reinterpreted to mean that biology only makes sense in the light of adaptation. Some philosophers of science have argued in this spirit that all work in ‘proximal’ biosciences such as anatomy, physiology and molecular biology must be framed, at least implicitly, by the selection histories of the organisms under study. Others have denied this and have proposed non-evolutionary ways in which (...) biologists can frame these investigations. This paper argues that an evolutionary perspective is indeed necessary, but that it must be a forward-looking perspective informed by a general understanding of the evolutionary process, not a backward-looking perspective informed by the specific evolutionary history of the species being studied. Interestingly, it turns out that there are aspects of proximal biology that even a creationist cannot study except in the light of a theory of their effect on future evolution. (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)

By linking the concepts of homology and morphological organization to evolvability, this paper attempts to (1) bridge the gap between developmental and phylogenetic approaches to homology and to (2) show that developmental constraints and natural selection are compatible and in fact complementary. I conceive of a homologue as a unit of morphological evolvability, i.e., as a part of an organism that can exhibit heritable phenotypic variation independently of the organism’s other homologues. An account of homology therefore consists in explaining how (...) an organism’s developmental constitution results in different homologues/characters as units that can evolve independently of each other. The explanans of an account of homology is developmental, yet the very explanandum is an evolutionary phenomenon: evolvability in a character-by-character fashion, which manifests itself in phylogenetic patterns as recognized by phylogenetic approaches to homology. While developmental constraints and selection have often been viewed as antagonistic forces, I argue that both are complementary as they concern different parts of the evolutionary process. Developmental constraints, conceived of as the presence of the same set of homologues across phenotypic change, pertain to how heritable variation can be generated in the first place (evolvability), while natural selection operates subsequently on the produced variation. (shrink)

Mnoge biološke funkcije dopuštaju stupnjevanje. Na primjer, lučenje određenog hormona u organizmu može biti na višoj ili nižoj razini, u usporedbi s istim organizmom drugom prilikom ili u usporedbi s drugim organizmima. Koje razine funkcioniranja predstavljaju slučajeve disfunkcije; gdje da povučemo crtu? To je kvantitativni problem za teorije disfunkcije i bolesti. Cilj mi je braniti verziju bioloških teorija disfunkcije kako bih se uhvatio u koštac s ovim problemom. Međutim, također ću dopustiti da evaluativna razmatranja uđu u teoriju bolesti. Moj argument (...) se temelji na razlikovanju između biološke i kliničke perspektive. Prema mom mišljenju, bolest je ograničena na slučajeve koji spadaju u granice bioloških disfunkcija. Odgovor na kvantitativni problem ne zahtijeva proizvoljne odluke ili društveno vrijednosne sudove. Stoga se zalažem za nearbitrarnu metodu koja se temelji na činjenicama kako bi se riješio kvantitativni problem. Ipak, nisu sve biološke disfunkcije instance bolesti. Dodavanje kliničke perspektive omogućuje nam da spriječimo potencijalnu preveliku uključenost biološke perspektive, zato što postavlja dodatna ograničenja za određivanje granica bolesti. (shrink)

Philosophical discussions of biological classification have failed to recognise the central role of homology in the classification of biological parts and processes. One reason for this is a misunderstanding of the relationship between judgments of homology and the core explanatory theories of biology. The textbook characterisation of homology as identity by descent is commonly regarded as a definition. I suggest instead that it is one of several attempts to explain the phenomena of homology. Twenty years ago the ‘new experimentalist’ movement (...) in philosophy of science drew attention to the fact that many experimental phenomena have a ‘life of their own’: the conviction that they are real is not dependent on the theories used to characterise and explain them. I suggest that something similar can be true of descriptive phenomena, and that many homologies are phenomena of this kind. As a result the descriptive biology of form and function has a life of its own—a degree of epistemological independence from the theories that explain form and function. I also suggest that the two major ‘homology concepts’ in contemporary biology, usually seen as two competing definitions, are in reality complementary elements of the biological explanation of homology. (shrink)

Teleosemantics attempts to explain the content of mental representations through an appeal to functions, and typically attributes function to selection history. The narrowest cases focus on only evolutionary fitness benefit through natural selection, while broader theories have come to accept multiple levels of selection, including those over the course of a lifetime such as neural selection. The precise way to define function has given rise to many debates over the content of hypothetical mental representations. In this paper, I argue that (...) defining function through the lens of Nikolas Tinbergen’s levels of analysis provides a valuable framework in organizing and analyzing teleological theories of function, and can advance the debate into a more organized discourse. In particular, after defining and defending them on theoretical grounds, I go through three classic teleosemantic debates about content ascription and function and attempt to organize them in a Tinbergian framework in order to demonstrate their general applicability, followed by two more examples from humans and primates in order to give insight on the role of each level of analysis in cases where we have more direct internal access to the content of such representations. I finally suggest that a pluralist viewpoint of the content of representations in complex organisms may be justified. I argue that in light of Tinbergen’s levels of analysis framework, teleosemantic theories of mental content can be more clearly discussed and advanced. (shrink)

These preprints were automatically compiled into a PDF from the collection of papers deposited in PhilSci-Archive in conjunction with the PSA 2018.

The traditional practice of establishing morphological types and investigating morphological organization has found new support from evolutionary developmental biology (evo-devo), especially with respect to the notion of body plans. Despite recurring claims that typology is at odds with evolutionary thinking, evo-devo offers mechanistic explanations of the evolutionary origin, transformation, and evolvability of morphological organization. In parallel, philosophers have developed non-essentialist conceptions of natural kinds that permit kinds to exhibit variation and undergo change. This not only facilitates a construal of species (...) and higher taxa as natural kinds, but also broadens our perspective on the diversity of kinds found in biology. There are many different natural kinds relevant to the investigative and explanatory aims of evo-devo, including homologues and developmental modules. (shrink)

Following Mayr (1961) evolutionary biologists often maintain that the hallmark of biology is its evolutionary perspective. In this view, biologists distinguish themselves from other natural scientists by their emphasis on why-questions. Why-questions are legitimate in biology but not in other natural sciences because of the selective character of the process by means of which living objects acquire their characteristics. For that reason, why-questions should be answered in terms of natural selection. Functional biology is seen as a reductionist science that applies (...) physics and chemistry to answer how-questions but lacks a biological point of view of its own. In this paper I dispute this image of functional biology. A close look at the kinds of issues studied in biology and at the way in which these issues are studied shows that functional biology employs a distinctive biological perspective that is not rooted in selection. This functional perspective is characterized by its concern with the requirements of the life-state and the way in which these are met. (shrink)

Karen Neander’s (1991a, b) Selected Effects (SE) theory of biological proper functions argues that the function of a trait is the action for which it was “caused” to be selected by natural selection. Her life’s work has already left a lasting impact, however SE theory has yet to be more properly formalized as a conceptual analysis of biological functions. Although other SE theories have sought to build upon Neander’s work (e.g., Garson, 2017), there remains an ambiguity in the theory’s use (...) of causal descriptors. For the success of her successors, delineating the function of causality for SE theory is of utmost importance. Here, I systematize Neander’s theory according to the different senses of causation inherent to it. I argue that structuring SE theory in terms of causal transitivity and intransitivity reveals that Neander’s analysis not only supersedes her detractors but likely exposes areas of vulnerability in others’ SE theory derivatives. (shrink)

In this paper we assess the explanatory role of idealizations in ‘design explanations’, a type of functional explanation used in biology. In design explanations, idealizations highlight which factors make a difference to phenomena to be explained: hypothetical, idealized, organisms are invoked to make salient which traits of extant organisms make a difference to organismal fitness. This result negates the view that idealizations serve only pragmatic benefits, and complements the view that idealizations highlight factors that do not make a difference. This (...) analysis in particular strengthens the perspective that idealizations are means to highlight difference making factors, and identifies a novel, more direct role for idealizations in doing so. It thus offers a novel argument why in some explanatory contexts idealizations are in-eliminable. (shrink)

Comparative biology builds up systematic knowledge of the diversity of life, across evolutionary lineages and levels of organization, starting with evidence from a sparse sample of model organisms. In developmental biology, a key obstacle to the growth of comparative approaches is that the concept of homology is not very well defined for levels of organization that are intermediate between individual genes and morphological characters. In this paper, we investigate what it means for ontogenetic processes to be homologous, focusing specifically on (...) the examples of insect segmentation and vertebrate somitogenesis. These processes can be homologous without homology of the underlying genes or gene networks, since the latter can diverge over evolutionary time, while the dynamics of the process remain the same. Ontogenetic processes like these therefore constitute a dissociable level and distinctive unit of comparison requiring their own specific criteria of homology. In addition, such processes are typically complex and nonlinear, such that their rigorous description and comparison not only requires observation and experimentation, but also dynamical modeling. We propose six criteria of process homology, combining recognized indicators with novel ones derived from dynamical systems modeling. We show how these criteria apply to animal segmentation and other ontogenetic processes. We conclude by situating our proposed dynamical framework for homology of process in relation to similar research programs, such as process structuralism and developmental approaches to morphological homology. (shrink)

In the recent literature on explanation in biology, increasing attention is being paid to the connection between design explanation and mechanistic explanation, viz. the role of design principles and heuristics for mechanism discovery and mechanistic explanation. In this paper we extend the connection between design explanation and mechanism discovery by prizing apart two different types of design explanation and by elaborating novel heuristics that one specific type offers for mechanism discovery across species. We illustrate our claims in terms of two (...) lines of biological research on the biological advantages of organismal traits, one on the eye-size of giant squid, the other on foraging habits of specific bat species. We argue that this research illustrates useful heuristics for mechanism discovery across species, viz. reasoning strategies to infer likely mechanisms for a certain biological role based on assessments of the environmental conditions in which the role is performed efficiently and less or in-efficiently. We bring out the novel features of our analysis in terms of a comparison with mechanistic approaches to mechanism discovery, amongst which graph-theoretical ones, and by comparing the different types of design explanation and the discovery heuristics they support. (shrink)

Current philosophical theorizing about technical functions is mainly focused on specifying conditions under which agents are justified in ascribing functions to technical artifacts. Yet, assessing the precise explanatory relevance of such function ascriptions is, by and large, a neglected topic in the philosophy of technical artifacts and technical functions. We assess the explanatory utility of ascriptions of technical functions in the following three explanation-seeking contexts: why was artifact x produced?, why does artifact x not have the expected capacity to ϕ?, (...) how does artifact x realize its capacity to ϕ? We argue that while function ascriptions serve a mere heuristic role in the first context, they have substantial explanatory leverage in the second and third context. In addition, we assess the relevance of function ascriptions in the context of engineering redesign. Here, function ascriptions also play a relevant role: they enable normative statements of the sort that component b functions better than component a. We unpack these claims by considering philosophical theories of technical functions, in particular the ICE theory, and engineering work on function ascription and explanation. We close the paper by relating our analysis to current debates on the explanatory power of mechanistic vis-à-vis functional explanations. (shrink)

In the last few years, the lack of a unitary notion of gene across biological sciences has troubled the philosophy of biology community. However, the debate on this concept has remained largely historical or focused on particular cases presented by the scientific empirical advancements. Moreover, in the literature there are no explicit and reasonable arguments about why a philosophical clarification of the concept of gene is needed. In our paper, we claim that a philosophical clarification of the concept of gene (...) does not contribute to biology. Unlike the question, for example, “What is a biological function?”, we argue that the question “What is a gene?” could be answered by means of empirical research, in the sense that biologists' labour is enough to shed light on it. (shrink)

This paper is concerned with reasonings that purport to explain why certain organisms have certain traits by showing that their actual design is better than contrasting designs. Biologists call such reasonings 'functional explanations'. To avoid confusion with other uses of that phrase, I call them 'design explanations'. This paper discusses the structure of design explanations and how they contribute to scientific understanding. Design explanations are contrastive and often compare real organisms to hypothetical organisms that cannot possibly exist. They are not (...) causal but appeal to functional dependencies between an organism's different traits. These explanations point out that because an organism has certain traits, it cannot be alive if the trait to be explained were replaced by a specified alternative. They can be understood from a mechanistic point of view as revealing the constraints on what mechanisms can be alive. (shrink)

In its last round of publications in September 2012, the Encyclopedia Of DNA Elements (ENCODE) assigned a biochemical function to most of the human genome, which was taken up by the media as meaning the end of ‘Junk DNA’. This provoked a heated reaction from evolutionary biologists, who among other things claimed that ENCODE adopted a wrong and much too inclusive notion of function, making its dismissal of junk DNA merely rhetorical. We argue that this criticism rests on misunderstandings concerning (...) the nature of the ENCODE project, the relevant notion of function and the claim that most of our genome is junk. We argue that evolutionary accounts of function presuppose functions as ‘causal roles’, and that selection is but a useful proxy for relevant functions, which might well be unsuitable to biomedical research. Taking a closer look at the discovery process in which ENCODE participates, we argue that ENCODE’s strategy of biochemical signatures successfully identified activities of DNA elements with an eye towards causal roles of interest to biomedical research. We argue that ENCODE’s controversial claim of functionality should be interpreted as saying that 80 % of the genome is engaging in relevant biochemical activities and is very likely to have a causal role in phenomena deemed relevant to biomedical research. Finally, we discuss ambiguities in the meaning of junk DNA and in one of the main arguments raised for its prevalence, and we evaluate the impact of ENCODE’s results on the claim that most of our genome is junk. (shrink)

Ethics, Policy & Environment, Volume 14, Issue 3, Page 329-344, October 2011.

In this article we offer a detailed assessment of current approaches to the origins of language, with a special foots on their historical and theoretical underpinnings. It is a widely accepted view within evolutionary linguistics that an account of the emergence of human language necessarily involves paying special attention to its communicative function and its relation to other animal communication systems. Ever since Darwin, some variant of this view has constituted the mainstream version in evolutionary linguistics; however, it is our (...) contention in this article that this approach is seriously flawed, and that “animal communication” does not constitute a natural kind on which a sound theoretical model can be built. As a consequence, we argue that this communicative perspective is better abandoned in favor of a structural/formal approach based on the notion of homology, and that some interesting and unexpected similarities may be found by applying this venerable comparative method founded in the 19th century by Richard Owen. (shrink)