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)

Empirical adaptationism is often said to be an empirical claim about nature, which concerns the overall relative causal importance of natural selection in evolution compared with other evolutionary factors. Philosophers and biologists who have tried to clarify the meaning of empirical adaptationism usually share, explicitly or implicitly, two assumptions: (1) Empirical adaptationism is an empirical claim that is scientifically testable; (2) testing empirical adaptationism is scientifically valuable. In this article, I challenge these two assumptions and argue that both are unwarranted (...) given how empirical adaptationism is currently formulated. I identify a series of conceptual and methodological difficulties that makes testing empirical adaptationism in a biologically non-arbitrary way virtually impossible. Moreover, I show that those in favor of testing empirical adaptationism have yet to demonstrate the distinctive value and necessity of conducing such a test. My analysis of the case of empirical adaptationism also provides reasons for scientists to reconsider the value and necessity of engaging in scientific debates involving the notion of overall relative causal importance. (shrink)

This paper will critically assess Popper’s evolutionary philosophy. There exists a rich literature on the topic with which we have many reservations. We believe that Popper’s evolutionary philosophy should be assessed in light of the intriguing theoretical insights offered, during the last 10 years or so, by the philosophy of biology, evolutionary biology and molecular biology. We will argue that, when analysed in this manner, Popper’s ideas concerning the nature of selection, Lamarckism and the theoretical limits of neo-Darwinism can be (...) appreciated in their full biological and philosophical value. (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)

There is a trend within philosophy of biology to concentrate on questions that are strongly related to particular biological research programs rather than on the general scope of the field and its relation to other sciences. Projects of the latter kind, of course, are followed as well but will not be the topic of this review. Shifting the focus to particular research programs reflects philosophers’ increased interest in knowledge of, and contribution to, actual biological research, which is organized in such (...) programs. It is accompanied by the increasing enthusiasm of biologists to involve philosophers in the conceptual work of theoretical biology. I concentrate on the philosophies of four biological research programs, three of which are devoted to evolutionary biology, which is still the main field of interest among philosophers of biology: adaptationism, EvoDevo, and the developmental systems approach. In addition, a short sketch of the newly emerging philosophy of systems biology is given. Several lines of philosophical inquiry can be found in all of the fields considered here: philosophy contributes to the conceptual development of biological research programs, it analyzes structures and delineations of particular research programs, and sometimes it is involved in a comparative assessment of biological programs as well. Philosophical projects that start from the level of a particular research program may give rise to a bottom-up perspective on biology and allow for an integrative view of biological research. This may open up the opportunity to tackle “larger” questions again in an altered and fruitful manner. (shrink)

We present two case studies from contemporary biology in which we observe conflicts between established and emerging approaches. The first case study discusses the relation between molecular biology and systems biology regarding the explanation of cellular processes, while the second deals with phylogenetic systematics and the challenge posed by recent network approaches to established ideas of evolutionary processes. We show that the emergence of new fields is in both cases driven by the development of high-throughput data generation technologies and the (...) transfer of modeling techniques from other fields. New and emerging views are characterized by different philosophies of nature, i.e. by different ontological and methodological assumptions and epistemic values and virtues. This results in a kind of conflict we call “epistemic competition” that manifests in two ways: On the one hand, opponents engage in mutual critique and defense of their fundamental assumptions. On the other hand, they compete for the acceptance and integration of the knowledge they provide by a broader scientific community. Despite an initial rhetoric of replacement, the views as well as the respective audiences come to be seen as more clearly distinct during the course of the debate. Hence, we observe—contrary to many other accounts of scientific change—that conflict results in the formation of new niches of research, leading to co-existence and perceived complementarity of approaches. Our model thus contributes to the understanding of the pluralization of the scientific landscape. (shrink)

Design thinking in general, and optimality modeling in particular, have traditionally been associated with adaptationism—a research agenda that gives pride of place to natural selection in shaping biological characters. Our goal is to evaluate the role of design thinking in non-evolutionary analyses. Specifically, we focus on research into abstract design principles that underpin the functional organization of extant organisms. Drawing on case studies from engineering-inspired approaches in biology we show how optimality analysis, and other design-related methods, play a specific methodological (...) role that is tangential to the study of adaptation. To account for the role of these reasoning strategies in contemporary biology, we therefore suggest a reevaluation of the connection between design thinking and adaptationism. (shrink)

Adaptationism has for decades been the topic of sophisticated debates in philosophy of biology but methodological adaptationism has not received as much attention as the empirical and explanatory issues. In addition, adaptationism has mainly been discussed in the context of evolutionary biology and not in fields such as zoophysiology and systems biology where this heuristic is also used in design analyses of physiological traits and molecular structures. This paper draws on case studies from these fields to discuss the productive and (...) problematic aspects of this heuristic in different research practices, in functional as well as evolutionary studies on different levels of biological organization. Gould and Lewontin’s Spandrels-paper famously criticized adaptationist methodology for implying the risk of generating ‘blind spots’ with respect to non-selective effects on evolution. Some have claimed that this bias can be accommodated through the testing of evolutionary hypotheses. Although this is an important aspect of overcoming naïve adaptationism, I argue that the issue of methodological biases is broader than the question of testability. I demonstrate the productivity of adaptationist heuristics but also discuss the deeper problematic aspects associated with the methodological imperialism that is part of the strong adaptationist position. (shrink)

The purpose of this paper is to defend, contra Fodor and Piattelli-Palmarini (F&PP), that the theory of natural selection (NS) is a perfectly bona fide empirical unified explanatory theory. F&PP claim there is nothing non-truistic, counterfactual-supporting, of an “adaptive” character and common to different explanations of trait evolution. In his debate with Fodor, and in other works, Sober defends NS but claims that, compared with classical mechanics (CM) and other standard theories, NS is peculiar in that its explanatory models are (...) a priori (a trait shared with few other theories). We argue that NS provides perfectly bona fide adaptive explanations of phenotype evolution, unified by a common natural-selection guiding principle. First, we introduce the debate and reply to F&PP’s main argument against NS. Then, by reviewing different examples and analyzing Fisher’s model in detail, we show that NS explanations of phenotypic evolution share a General Natural Selection Principle. Third, by elaborating an analogy with CM, we argue against F&PP’s claim that such a principle would be a mere truism and thus explanatorily useless, and against Sober’s thesis that NS models/explanations have a priori components that are not present in CM and other common empirical theories. Irrespective of differences in other respects, the NS guiding principle has the same epistemic status as other guiding principles in other highly unified theories such as CM. We argue that only by pointing to the guiding principle-driven nature that it shares with CM and other highly unified theories, something no-one has done yet in this debate, one can definitively show that NS is not defective in F&PP’s sense: in the respects relevant to the debate, Natural Selection is as defective and as epistemically peculiar as Classical Mechanics and other never questioned theories. (shrink)

The Linda paradox is a key topic in current debates on the rationality of human reasoning and its limitations. We present a novel analysis of this paradox, based on the notion of verisimilitude as studied in the philosophy of science. The comparison with an alternative analysis based on probabilistic confirmation suggests how to overcome some problems of our account by introducing an adequately defined notion of verisimilitudinarian confirmation.

The ecologist today finds scarce ground safe from controversy. Decisions must be made about what combination of data, goals, methods, and theories offers them the foundations and tools they need to construct and defend their research. When push comes to shove, ecologists often turn to philosophy to justify why it is their approach that is scientific. Karl Popper’s image of science as bold conjectures and heroic refutations is routinely enlisted to justify testing hypotheses over merely confirming them. One of the (...) most controversial theories in contemporary science is the Neutral Theory of Ecology. Its chief developer and proponent, Stephen Hubbell, presents the neutral theory as a bold conjecture that has so far escaped refutation. Critics of the neutral theory claim that it already stands refuted, despite what the dogmatic neutralists say. We see the controversy through a Popperian lens. But Popper’s is an impoverished philosophy of science that distorts contemporary ecology. -/- The controversy surrounding the neutral theory actually rests on a methodological fault. There is a strong but messy historical link between the concepts of being neutral and being null in biology, and Hubbell perpetuates this when he claims that the neutral theory is supplies the appropriate null for testing alternative theories. What method is being followed here? There are three contenders: -/- Null hypothesis testing tests for whether a there is a pattern to be explained. Null modeling tests for whether a process is causally relevant to a pattern. Baseline modeling apportions relative responsibility to multiple processes each relevant to a pattern. -/- Whether the neutral theory supplies an appropriate “null” depends upon whether null hypothesis, null modeling, or baseline model is intended. These methods prescribe distinct inference patterns. If they are null hypothesis testing or null modeling, the neutralists’s reasoning is invalid. If they are baseline modeling, the justification of a crucial assumption remains opaque. Either way, the neutral-null connection is being exploited rhetorically to privilege the neutral theory over its rivals. Clarifying the reasoning immunizes us against the rhetoric and foregrounds the underlying virtues of the neutralist approach to ecology. -/- The Popperian lens distorts theoretical development as dogmatism. Lakatos’s view of science as the development of research programmes clarifies the epistemology of the neutral theory. Focusing philosophical attention on the neutralist research programme illuminates (1) the synchronic uses of the neutral theory to make predictions and give descriptions and explanations; (2) its diachronic development in response to theoretical innovation and confrontation with data; (3) its complex relationships to alternative theories. For example, baseline modeling is now seen to be its primary explanatory heuristic. The justification for baseline modeling with the neutral theory, previously hidden from view, is seen in the logic of in the neutralist research programme. (shrink)

Systems biology is sometimes presented as providing a superior approach to the problem of biological complexity. Its use of ‘unbiased’ methods and formal quantitative tools might lead to the impression that the human factor is effectively eliminated. However, a closer look reveals that this impression is misguided. Systems biologists cannot simply assemble molecular information and compute biological behavior. Instead, systems biology’s main contribution is to accelerate the discovery of mechanisms by applying models as heuristic tools. These models rely on a (...) variety of idealizing and simplifying assumptions in order to be efficient for this purpose. The strategies of systems biologists are similar to those of experimentalists in that they attempt to reduce the complexity of the discovery process. Analyzing and comparing these strategies, or ‘heuristics’, reveals the importance of the human factor in computational approaches and helps to situate systems biology within the epistemic landscape of the life sciences. (shrink)

Segundo Daniel Dennett insistiu em diferentes trabalhos, o programa adaptacionista darwiniano constitui uma legítima e insubstituível translação da perspectiva intencional ao domínio da biologia. Mas, para que essa tese possa ser formulada com toda clareza, e não fique no plano da simples metáfora – coisa que não é o objetivo de Dennett – é necessário esclarecer qual seria o sistema intencional cujo comportamento estudamos conforme essa perspectiva. Assim, e contra a alternativa escolhida pelo próprio Dennett, e retomando uma proposta do (...) Karl Popper, sustentaremos que esse sistema não é a natureza como um tudo, mas sim o sistema constituído por uma população ou uma linhagem de organismos: eles são os agentes dos processos adaptativos. Não é nossa meta, entretanto, contradizer as teses centrais da Dennett; mas sim as reforçar.How do species think? Daniel Dennett has insisted in different occasions that Darwin’s Adaptationist Program constitutes a legitimate and hardly displaceable translation of the intentional point of view in the Biology field. However, in order for us to be able to state this thesis clearly and to avoid getting into the domain of mere metaphor – which is not Dennett’s purpose -, we have to single out what intentional system the behaviour of which we study on such a perspective. That being noted, we shall argue, contrary to the alternative that Dennett himself picked out, and close to Karl Popper’s suggestion, that such a system is not nature as a whole, but the system made up by a population or a class of organisms: those are the agents of the adaptative processes. We do not, however, aim at contradicting Dennett’s overall strategy; rather, we aim at reinforcing it. (shrink)