Several prominent debates in biology, such as those surrounding adaptationism, group selection, and punctuated equilibrium, have focused on disagreements about the relative importance of a cause in producing a phenomenon of interest. Some philosophers, such as John Beatty have expressed scepticism about the scientific value of engaging in these controversies, and Karen Kovaka has suggested that their value might be limited. In this paper, I challenge that scepticism by giving a novel analysis of relative significance controversies, showing that there are (...) three forms they can take. I argue that these controversies can have significant epistemic upshots, in that they help scientists form predictions about new instances of the phenomenon of interest. Finally, using two historical examples, I show how engaging in these controversies can improve our understanding of causal relationships. (shrink)

Si bien en la filosofía de las ciencias ya se han explorado algunos ejemplos provenientes de la bioquímica como casos de estudio, la filosofía de la bioquímica es una subdisciplina naciente. En este artículo estudiaremos dos problemas filosóficos de relevancia contemporánea en esta ciencia. Por un lado, examinaremos las bases epistemológicas del problema del plegamiento de proteínas. En particular lo relacionado con la predicción de la estructura tridimensional de las proteínas a partir de su secuencia, asunto que ha dado mucho (...) que hablar debido a los nuevos avances utilizando deep learning. Por otro lado, exploraremos el problema in-vitro/in-vivo y, más generalmente, el problema de la extrapolación en las ciencias biológicas. Finalmente, a partir de las consecuencias de ambos temas consideraremos algunas reflexiones filosóficas generales acerca del reduccionismo, el pluralismo y el lugar de la bioquímica en las ciencias biológicas. Palabras clave: Bioquímica, Plegamiento de proteínas, In-vitro/in-vivo, Pluralismo, Reduccionismo. (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)

What methodological approaches do research programs use to investigate the world? Elisabeth Lloyd’s Logic of Research Questions (LRQ) characterizes such approaches in terms of the questions that the researchers ask and causal factors they consider. She uses the Logic of Research Questions Framework to criticize adaptationist programs in evolutionary biology for dogmatically assuming selection explanations of the traits of organisms. I argue that Lloyd’s general criticism of methodological adaptationism is an artefact of the impoverished LRQ. My Ordered Factors Proposal extends (...) the LRQ to characterize approaches with sequences of questions and factors. I highlight the importance that ordering one’s investigation plays in approaches at the level of adaptationism by analyzing two research programs in community ecology: competitionists and neutralists. Competitionists and neutralists take opposed starting points and use explanatory and developmental heuristics to consider more factors in due time. On the Ordered Factors Proposal, these approaches are not only the ecological factors they are open to considering but also the order in which they will consider them. My disagreement with Lloyd’s over how to characterize methodological approaches reflects different views about methodological monism and pluralism. (shrink)

In this review, we describe some of the central philosophical issues facing origins-of-life research and provide a targeted history of the developments that have led to the multidisciplinary field of origins-of-life studies. We outline these issues and developments to guide researchers and students from all fields. With respect to philosophy, we provide brief summaries of debates with respect to (1) definitions (or theories) of life, what life is and how research should be conducted in the absence of an accepted theory (...) of life, (2) the distinctions between synthetic, historical, and universal projects in origins-of-life studies, issues with strategies for inferring the origins of life, such as (3) the nature of the first living entities (the “bottom up” approach) and (4) how to infer the nature of the last universal common ancestor (the “top down” approach), and (5) the status of origins of life as a science. Each of these debates influences the others. Although there are clusters of researchers that agree on some answers to these issues, each of these debates is still open. With respect to history, we outline several independent paths that have led to some of the approaches now prevalent in origins-of-life studies. These include one path from early views of life through the scientific revolutions brought about by Linnaeus (von Linn.), Wöhler, Miller, and others. In this approach, new theories, tools, and evidence guide new thoughts about the nature of life and its origin.We also describe another family of paths motivated by a” circularity” approach to life, which is guided by such thinkers as Maturana & Varela, Gánti, Rosen, and others. These views echo ideas developed by Kant and Aristotle, though they do so using modern science in ways that produce exciting avenues of investigation. By exploring the history of these ideas, we can see how many of the issues that currently interest us have been guided by the contexts in which the ideas were developed. The disciplinary backgrounds of each of these scholars has influenced the questions they sought to answer, the experiments they envisioned, and the kinds of data they collected. We conclude by encouraging scientists and scholars in the humanities and social sciences to explore ways in which they can interact to provide a deeper understanding of the conceptual assumptions, structure, and history of origins-of-life research. This may be useful to help frame future research agendas and bring awareness to the multifaceted issues facing this challenging scientific question. (shrink)

Neutral Theory is controversial in ecology. Ecologists and philosophers have diagnosed the source of the controversy as: its false assumption that individuals in different species within the same trophic level are ecologically equivalent, its conflict with Competition Theory and the adaptation of species, its role as a null hypothesis, and as a Lakatosian research programme. In this paper, I show why we should instead understand the conflict at the level of research programs which involve more than theory. The Neutralist and (...) Competitionist research programs borrow and construct theories, models, and experiments for various aims and given their home ecological systems. I present a holistic and pragmatic view of the controversy that foregrounds the interrelation between many kinds of practices and decisions in ecological research. (shrink)

We identify a species of experiment—Kon-Tiki experiments—used to demonstrate the competence of a cause to produce a certain effect, and we examine their role in the historical sciences. We argue that Kon-Tiki experiments are used to test middle-range theory, to test assumptions within historical narratives, and to open new avenues of inquiry. We show how the results of Kon-Tiki experiments are involved in projective inferences, and we argue that reliance on projective inferences does not provide historical scientists with any special (...) protection against the problem of unconceived alternatives. (shrink)

It is widely acknowledged that metaphysical assumptions, commitments and presuppositions play an important role in science. Yet according to the empiricist there is no place for metaphysics as traditionally understood in the scientific enterprise. In this paper I aim to take a first step towards reconciling these seemingly irreconcilable claims. In the first part of the paper I outline a conception of metaphysics and its relation to science that should be congenial to empiricists, motivated by van Fraassen’s work on ‘stances’. (...) There has been a considerable amount of recent work devoted to van Fraassen’s ‘stance’ view, but it has not on the whole been noticed that the view has the potential to motivate a general empiricist conception of the relation between science and metaphysics. In the second and third sections I discuss two examples from biology to illustrate this conception: metaphysical punctuationism, and its relation to and influence on the thesis of punctuated equilibrium; and dialectical biology as defended by Levins and Lewontin. (shrink)

Abstract.Evolutionary psychology and behavioural genomics are both approaches to explain human behaviour from a genetic point of view. Nonetheless, thus far the development of these disciplines is anything but interdependent. This paper examines the question whether evolutionary psychology can contribute to behavioural genomics. Firstly, a possible inconsistency between the two approaches is reviewed, viz. that evolutionary psychology focuses on the universal human nature and disregards the genetic variation studied by behavioural genomics. Secondly, we will discuss the structure of biological explanations. (...) Some philosophers rightly acknowledge that explanations do not involve laws which are exceptionless and universal. Instead, generalisations that are invariant suffice for successful explanation as long as two other stipulations are recognised: the domain within which the generalisation has no exceptions as well as the distribution of the mechanism described by the generalisation should both be specified. It is argued that evolutionary psychology can contribute to behavioural genomic explanations by accounting for these two specifications. (shrink)

Recent discussion of mechanism has suggested new approaches to several issues in the philosophy of science, including theory structure, causal explanation, and reductionism. Here, I apply what I take to be the fruits of the Ônew mechanical philosophyÕ to an analysis of a contemporary debate in evolutionary biology about the role of natural selection in speciation. Traditional accounts of that debate focus on the geographic context of genetic divergence— namely, whether divergence in the absence of geographic isolation is possible (or (...) significant). Those accounts are at best incomplete, I argue, because they ignore the mechanisms producing divergence and miss what is at stake in the biological debate. I argue that the biological debate instead concerns the scope of particular speciation mechanisms which assign different roles to natural selection at various stages of divergence. The upshot is a new interpretation of the crux of that debate—namely, whether divergence with gene flow is possible (or significant) and whether the isolating mechanisms producing it are adaptive. Ó 2005 Elsevier Ltd. All rights reserved. (shrink)

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)

‘Gouldian arguments’ appeal to the contingency of a scientific domain to establish that domain’s autonomy from some body of theory. For instance, pointing to evolutionary contingency, Stephen Jay Gould suggested that natural selection alone is insufficient to explain life on the macroevolutionary scale. In analysing contingency, philosophers have provided source-independent accounts, understanding how events and processes structure history without attending to the nature of those events and processes. But Gouldian Arguments require source-dependent notions of contingency. An account of contingency is (...) source-dependent when it is indexed to some pattern and some process. Positions like Gould’s do not turn on the mere fact of life’s contingency—that life’s shape could have been different due to its sensitivity to initial conditions, path-dependence or stochasticity. Rather, Gouldian arguments require that the contingency is due to particular kinds of processes: in this case, those which microevolutionary theory cannot account for. This source-dependent perspective clarifies both debates about the nature and importance of contingency, and empirical routes for testing Gould’s thesis. (shrink)

Introduction: the neuroscientific turn in political science The observation that brains and political orders are interdependent is almost trivial. Obviously, political orders require brain processes in order to emerge and to remain in place, as these processes enable action and cognition. Conversely, every since Aristotle coined man as “by nature a political animal” (Aristotle, Pol.: 1252a 3; cf. Eth. Nic.: 1097b 11), this also suggests that the political engagements of this animal has likely consequences for its natural development, including the (...) development of its psychological functions. Given these mutual interdependencies, it is remarkable that only since the 1960s, the more general domain of ‘biopolitics’ has attracted attention though first particularly in the form of behavioral politics (Alford and Hibbing). Since then biopolitics has gained in interest, so much so that different subdomains can be identified. Indeed, a 2008 review of the field of biopolitics identified five ‘headings’ of it: “(1) the case for a ‘more biologically oriented political science’, (2) ‘biologically related’ public policy issues, (3) physiological measures of political attitudes and behaviour, (4) the influence of physiological factors on actual political behaviour, and (5) the manner in which our species’ evolutionary history has left homo sapiens genetically endowed with certain social and political behavioural tendencies” (Somit and Peterson 43). Striking is how the relation between biology and politics is taken here in a rather unidirectional way, emphasizing particularly the decisive power of biology upon politics. The reverse relation is not mentioned specifically, reflecting the field of biopolitics, perhaps until quite recently. This absence of studies of political influences on our biology may have to do with the difficulty in investigating such influences. Empirical studies in biopolitics have two foci, broadly speaking: genetics and the brain, both of which have turned out to be complex and dynamic phenomena (Alford and Hibbing). Yet the studies of genetics and brain processes have made much progress in the last few decades, thanks to the development of research instruments - like fMRI brain scanners and TMS brain stimulation instruments - and of computational tools for data analysis and the simulation of explanatory models. For the field of biopolitics it is particularly relevant that within cognitive neuroscience the study of social and political issues has witnessed an increasing interest of researchers even more recently. Indeed, aware of the enabling and mediating role of the brain regarding those issues, a truly ‘neuroscientific turn’ can be observed in the social sciences, testified for example by the emergence of the field of ‘neuropolitics’ (Connolly; Vandervalk). Developing a systematic neuropolitics or biopolitics in general is a difficult challenge because of the wealth of causal influences on and interdependencies between biological, brain, cognitive and socio-political factors. Taking a somewhat more abstract perspective, this paper focuses on the process of emerging complexity in adaptive systems, enabling those to conduct ever more complex processes. Yet, parallel to that development can be observed that such systems, or organisms, are also capable in reducing the complexity of the information they are to process. Once they’re capable of developing and adjusting such compressed and complex representations of information, those systems or organisms can handle more information faster and more efficient and adaptive, yielding important benefits to the organism in navigating its environment (Halford, Wilson and Phillips). Before focusing on the role of narrative as a cognitive strategy for such a reduction of informational complexity, I will discuss the development of stable structures and increasing complexity in dynamic systems. Such a more general perspective prepares our discussion of the structures of both narratives and politics and in doing so contributes to the explanation of their interaction. (shrink)

Humans are capable of understanding an incredible variety of actions performed by other humans. Even though these range from primary biological actions, like eating and fleeing, to acts in parliament or in poetry, humans generally can make sense of each other’s actions. Action understanding is the cognitive ability to make sense of another person’s action by integrating perceptual information about the behavior with knowledge about the immediate and sociocultural contexts of the action, understanding of relevant meanings and one’s own experience. (...) Given the importance of action understanding in every domain of human life and society, and in light of the complexities that surround it, a comprehensive scientific understanding of this capacity is needed. Scholars are increasingly dissatisfied with monodisciplinary approaches to understanding human action, like when an action is interpreted only in sociocultural terms while overlooking cognitive constraints, or when an action is understood in biological terms while neglecting its psychological impact on the agent. Recent interdisciplinary endeavors demonstrate how an interdisciplinary approach is possible when investigating complex functions like action understanding. Ever more insight is gained in the mutual influences between biological, cognitive and sociocultural processes that together contribute to action and action understanding. The purpose of this chapter is to describe how a ‘mechanistic explanation’, or a ‘mechanism-based explanation’ of action understanding provides a theoretical framework for integrating various and often conflicting disciplinary insights. By applying the heuristics of ‘definition’, ‘decomposition’ and ‘localization’, researchers can determine the phenomenon that they collaboratively investigate while at the same time dividing this task into smaller component tasks of which the results must eventually be put together. Some researchers, for example, can apply a hermeneutic approach to the sociocultural environment in which action understanding takes place, while others aim to specify the cognitive processes or the neuro-electrical pathways that are activated under those conditions. After having presented a step-by-step analysis of an interdisciplinary investigation of action understanding by way of developing a mechanistic explanation the chapter closes with some suggestions for testing its result and mentions some limitations of this approach. (shrink)

Confirmation in evolutionary biology depends on what biologists take to be the genuine rivals. Investigating what constrains the scope of biological possibility provides part of the story: explaining how possible helps determine what counts as a genuine rival and thus informs confirmation. To clarify the criteria for genuine rivalry I distinguish between global and local constraints on biological possibility, and offer an account of how-possibly explanation. To sharpen the connection between confirmation and explaining how possible I discuss the view that (...) formal inquiry can provide a kind of confirmation-theoretic support for evolutionary models, and offer an example of how-possibly explanation interacting with testing practice. (shrink)

Biological knowledge does not fit the image of science that philosophers have developed. Many argue that biology has no laws. Here I criticize standard normative accounts of law and defend an alternative, pragmatic approach. I argue that a multidimensional conceptual framework should replace the standard dichotomous law/ accident distinction in order to display important differences in the kinds of causal structure found in nature and the corresponding scientific representations of those structures. To this end I explore the dimensions of stability, (...) strength, and degree of abstraction that characterize the variety of scientific knowledge claims found in biology and other sciences. (shrink)

How can we explain the intentional nature of an expert’s actions, performed without immediate and conscious control, relying instead on automatic cognitive processes? How can we account for the differences and similarities with a novice’s performance of the same actions? Can a naturalist explanation of intentional expert action be in line with a philosophical concept of intentional action? Answering these and related questions in a positive sense, this dissertation develops a three-step argument. Part I considers different methods of explanations in (...) cognitive neuroscience (Bennett & Hacker’s philosophical, conceptual analysis; Marr’s three levels of explanation; Neural Correlates of Consciousness research; mechanistic explanation), defending ‘mechanistic explanation’ as a method that provides the necessary tools for integrating interdisciplinary insights into human action. Furthermore, a dynamic, explanatory mechanism allows the assessment of the impact of learning and development on expert action in a valuable way that other methods don’t. Part II continues by scrutinizing several cognitive neuroscientific theories of learning and development (neuroconstructivism; dual-processing theories; simulation theory; extended mind/cognition hypothesis), arguing for the complex interactions between different types of processing and different action representations involved in expert action performances. Moreover, according to our discussion of a particular ‘simulation theory’ these interactions can be influenced in several ways with the use of language, allowing an agent to configure a specific action representation for performance at a later stage. The results of Parts I and II are then applied in Part III to a parallel discussion of philosophical analyses of intentional action (discussing i.a. Frankfurt, Bratman, Pacherie and Ricoeur) and cognitive neuroscientific insights in it. Both approaches are found to converge in emphasizing the importance for an expert to develop stable patterns of actions that comply maximally not only with his intentions, but also with his motor expertise and with situational conditions. Consequently, his actions – automatic, or not – rely on this ‘sculpted space of actions’. (shrink)

This chapter contains sections titled: Highlights of Past Literature Current Work Future Work.

The cis-regulatory hypothesis is one of the most important claims of evolutionary developmental biology. In this paper I examine the theoretical argument for cis-regulatory evolution and its role within evolutionary theorizing. I show that, although the argument has some weaknesses, it acts as a useful example for the importance of current scientific debates for science education.

The discovery and ongoing investigation of microRNAs suggest important conceptual and methodological lessons for philosophers and historians of biology. This paper provides an account of miRNA research and the shift from viewing these tiny regulatory entities as minor curiosities to seeing them as major players in the post-transcriptional regulation of genes. Conceptually, the study of miRNAs is part of a broader change in understandings of genetic regulation, in which simple switch-like mechanisms were reinterpreted as aspects of complex cellular and genome-wide (...) processes. Among them are the activities of small RNAs, previously regarded as non-functional. Methodologically, the miRNA story suggests new ways of characterizing biological research that should prove helpful to philosophers of science who seek to develop more pluralistic, pragmatic models of scientific inquiry. miRNA research displays iterative movements between multiple modes of investigation that include not only the proposal and testing of hypotheses but also exploratory, technology-oriented and question-driven modes of research. As an exemplary story of scientific discovery and development, the miRNA case illustrates transitions from genetics to genomics and systems biology, and it shows how diverse configurations of research practice are related to major scientific advances. (shrink)

A crucial socio-political challenge for our age is how to rede!ne or extend group membership in such a way that it adequately responds to phenomena related to globalization like the prevalence of migration, the transformation of family and social networks, and changes in the position of the nation state. Two centuries ago Immanuel Kant assumed that international connectedness between humans would inevitably lead to the realization of world citizen rights. Nonetheless, globalization does not just foster cosmopolitanism but simultaneously yields the (...) development of new group boundaries. Group membership is indeed a fundamental issue in political processes, for: “the primary good that we distribute to one another is membership in some human community” – it is within the political community that power is being shared and, if possible, held back from non-members. In sum, it is appropriate to consider group membership a fundamental ingredient of politics and political theory. How group boundaries are drawn is then of only secondary importance. Indeed, Schmitt famously declared that “[e]very religious, moral, economic, ethical, or other antithesis transforms into a political one if it is suffciently strong to group human beings e#ectively according to friend and enemy”. Even though Schmitt’s idea of politics as being constituted by such antithetical groupings is debatable, it is plausible to consider politics among other things as a way of handling intergroup di#erences. Obviously, some of the group-constituting factors are more easily discernable from one’s appearance than others, like race, ethnicity, or gender. As a result, factors like skin color or sexual orientation sometimes carry much political weight even though individuals would rather con!ne these to their private lives and individual identity. Given the potential tension between the political reality of particular groupmembership defnitions and the – individual and political – struggles against those definitions and corresponding attitudes, citizenship and civic behavior becomes a complex issue. As Kymlicka points out, it implies for citizens an additional obligation to non-discrimination regarding those groups: “[t]his extension of non-discrimination from government to civil society is not just a shift in the scale of liberal norms, it also involves a radical extension in the obligations of liberal citizenship”. Unfortunately, empirical research suggests that political intolerance towards other groups “may be the more natural and ‘easy’ position to hold”. Indeed, since development of a virtue of civility or decency regarding other groups is not easy, as it often runs against deeply engrained stereotypes and prejudices, political care for matters like education is justified. Separate schools, for example, may erode children’s motivation to act as citizens, erode their capacity for it and!nally diminish their opportunities to experience transcending their particular group membership and behave as decent citizens. This chapter outlines a possible explanation for such consequences. That explanation will be found to be interdisciplinary in nature, combining insights from political theory and cognitive neuroscience. In doing so, it does not focus on collective action, even though that is a usual focus for political studies. For example, results pertaining to collective political action have demonstrated that the relation between attitudes and overt voting behavior or political participation is not as direct and strong as was hoped for. Several conditions, including the individual’s experiences, self-interest, and relevant social norms, turned out to interfere in the link between his or her attitude and behavior. Important as collective action is, this chapter is concerned with direct interaction between agents and the in$uence of group membership on such interaction – in particular joint action. Although politics does include many forms of action that require no such physical interaction, such physical interaction between individuals remains fundamental to politics – this is the reason why separate schooling may eventually undermine the citizenship of its isolated pupils. This chapter will focus on joint action, de!ned as: “any form of social interaction whereby two or more individuals coordinate their actions in space and time to bring about a change in the environment”. Cognitive neuroscienti!c evidence demonstrates that for such joint action to succeed, the agents have to integrate the actions and expected actions of the other person in their own action plans at several levels of speci!city. Although neuroscienti!c research is necessarily limited to simple forms of action, this concurs with a philosophical analysis of joint action, which I will discuss below. (shrink)

Evo-Devo exhibits a plurality of scientific “cultures” of practice and theory. When are the cultures acting—individually or collectively—in ways that actually move research forward, empirically, theoretically, and ethically? When do they become imperialistic, in the sense of excluding and subordinating other cultures? This chapter identifies six cultures – three /styles/ (mathematical modeling, mechanism, and history) and three /paradigms/ (adaptationism, structuralism, and cladism). The key assumptions standing behind, under, or within each of these cultures are explored. Characterizing the internal structure of (...) the cultures is necessary for understanding how they collaborate or compete, and how they are fragmented or integrated, in the rich interdisciplinary /trading zone/ (Galison 1997) of Evo-Devo. Evo-Devo is an important example of how science can progress through a radical plurality of perspectives and cultures. (shrink)

Humans are capable of understanding an incredible variety of actions performed by other humans. Even though these range from primary biological actions, like eating and fleeing, to acts in parliament or in poetry, humans generally can make sense of each other’s actions. Understanding other people’s actions is called action understanding, and it can transcend differences in race, gender, culture, age, and social and historical circumstances. Action understanding is the cognitive ability to make sense of another person’s action by integrating perceptual (...) information about the behavior with knowledge about the immediate and sociocultural contexts of the action and with one’s own experience. Scholars are increasingly dissatisfied with monodisciplinary approaches to understanding human action. Such one-sidedness can rest upon various motives. For example, “hermeneutic interpretations” of action understanding tend to emphasize historical and cultural influences while overlooking that ultimately such influences depend upon individual cognitive processes. This has provoked criticism of the corresponding assumption that humans are born as a “blank slate” and that culture is solely responsible for all cognitive contents. However, such critique in turn easily slides into an overemphasis on the biology of human nature and a denial of sociocultural influences on cognition (Pinker, 2003). Fortunately, recent interdisciplinary endeavors have shown that an interdisciplinary approach is preferable when investigating complex functions like action understanding. The purpose of this chapter is to propose a “mechanism-based explanation” of action understanding that will provide a theoretical framework for integrating various and often conflicting disciplinary insights. (shrink)

Laws in the special sciences are usually regarded to be non-universal. A theory of laws in the special sciences faces two challenges. (I) According to Lange's dilemma, laws in the special sciences are either false or trivially true. (II) They have to meet the ?requirement of relevance?, which is a way to require the non-accidentality of special science laws. I argue that both challenges can be met if one distinguishes four dimensions of (non-) universality. The upshot is that I argue (...) for the following explication of special science laws: L is a special science law just if (1) L is a system law, (2) L is quasi-Newtonian, and (3) L is minimally invariant. (shrink)

Selectionist evolutionary theory has often been faulted for not making novel predictions that are surprising, risky, and correct. I argue that it in fact exhibits the theoretical virtue of predictive capacity in addition to two other virtues: explanatory unification and model fitting. Two case studies show the predictive capacity of selectionist evolutionary theory: parallel evolutionary change in E. coli, and the origin of eukaryotic cells through endosymbiosis.

Biologists and philosophers have been extremely pessimistic about the possibility of demonstrating random drift in nature, particularly when it comes to distinguishing random drift from natural selection. However, examination of a historical case-Maxime Lamotte's study of natural populations of the land snail, Cepaea nemoralis in the 1950s - shows that while some pessimism is warranted, it has been overstated. Indeed, by describing a unique signature for drift and showing that this signature obtained in the populations under study, Lamotte was able (...) to make a good case for a significant role for drift. It may be difficult to disentangle the causes of drift and selection acting in a population, but it is not impossible. (shrink)

This paper considers recent heated debates led by Jerry A. Coyne andMichael J. Wade on issues stemming from the 1929–1962 R.A. Fisher-Sewall Wrightcontroversy in population genetics. William B. Provine once remarked that theFisher-Wright controversy is central, fundamental, and very influential.Indeed,it is also persistent. The argumentative structure of therecent (1997–2000) debates is analyzed with the aim of eliminating a logicalconflict in them, viz., that the two sides in the debates havedifferent aims and that, as such, they are talking past each other. (...) Given aphilosophical analysis of the argumentative structure of the debates,suggestions supportive of Wade's work on the debate are made that areaimed, modestly, at putting the persistent Fisher-Wright controversy on thecourse to resolution. (shrink)

It has been claimed that ceteris paribus laws, rather than strict laws are the proper aim of the special sciences. This is so because the causal regularities found in these domains are exception-ridden, being contingent on the presence of the appropriate conditions and the absence of interfering factors. I argue that the ceteris paribus strategy obscures rather than illuminates the important similarities and differences between representations of causal regularities in the exact and inexact sciences. In particular, a detailed account of (...) the types and degrees of contingency found in the domain of biology permits a more adequate understanding of the relations among the sciences. (shrink)

Throughout his career David Hull has sought to bring the philosophy of science into closer contact with science and especially with biological science (Hull 1969, 1997b). This effort has taken many forms. Sometimes it has meant ‘either explaining basic biology to philosophers or explaining basic philosophy to biologists’ (Hull 1996, p. 77). The first of these tasks, simple as it sounds, has been responsible for revolutionary changes. It is well known that traditional philosophy of science, modeled as it was on (...) theoretical physics, proved inadequate when philosophers turned their attention to biological science. Biological examples have driven major revisions of accounts of reduction (Hull 1974; Schaffner 1993, Ch. 9), laws of nature (Beatty et al. 1997), theories (Lloyd 1988) and natural kinds (Wilson 1999, Part III). Nor is explaining basic philosophy to biologists a task to be looked down upon. It is useful, not because philosophy has all the answers, but because scientists must think about how to do science, that is doing philosophy of science and scientists frequently reinvent philosophical views with known flaws. Early in his career Hull found biological systematists in the grip of a crude operationalism about scientific concepts and said so in the pages of Systematic Zoology (Hull 1968). For the next thirty years, as biologists debated the nature of species and the correct principles of classification, Hull added a philosophical note at the same congresses and in the same journals (Hull 1970, 1976, 1980, 1997a, 1999). (shrink)

This paper develops an account of explanation in biology which does not involve appeal to laws of nature, at least as traditionally conceived. Explanatory generalizations in biology must satisfy a requirement that I call invariance, but need not satisfy most of the other standard criteria for lawfulness. Once this point is recognized, there is little motivation for regarding such generalizations as laws of nature. Some of the differences between invariance and the related notions of stability and resiliency, due respectively to (...) Sandra Mitchell and Brian Skyrms, are explored. (shrink)

Beatty, Brandon, and Sober agree that biological generalizations, when contingent, do not qualify as laws. Their conclusion follows from a normative definition of law inherited from the Logical Empiricists. I suggest two additional approaches: paradigmatic and pragmatic. Only the pragmatic represents varying kinds and degrees of contingency and exposes the multiple relationships found among scientific generalizations. It emphasizes the function of laws in grounding expectation and promotes the evaluation of generalizations along continua of ontological and representational parameters. Stability of conditions (...) and strength of determination in nature govern projectibility. Accuracy, ontological level, simplicity, and manageability provide additional measures of usefulness. (shrink)

The four case studies on chance in evolution provide a rich source for further philosophical analysis. Among the issues raised are the following: Are there different conceptions of chance at work, or is there a common underlying conception? How can a given concept of chance be distinguished from other chance concepts and from nonchance concepts? How can the occurrence of a given chance process be distinguished empirically from nonchance processes or other chance processes? What role does chance play in evolutionary (...) theory? I argue that in order to answer these questions, a careful distinction between process and outcome must be made; however, the purpose of this essay is not to answer these questions definitively, but rather to elaborate on them and to provide a starting point for further discussion. (shrink)

This is the second of a two-part essay on the history of debates concerning the creativity of natural selection, from Darwin through the evolutionary synthesis and up to the present. In the first part, I focussed on the mid-late nineteenth century to the early twentieth, with special emphasis on early Darwinism and its critics, the self-styled “mutationists.” The second part focuses on the evolutionary synthesis and some of its critics, especially the “neutralists” and “neo-mutationists.” Like Stephen Gould, I consider the (...) creativity of natural selection to be a key component of what has traditionally counted as “Darwinism.” I argue that the creativity of natural selection is best understood in terms of selection initiating evolutionary change, and selection directing evolutionary change, for example by creating the variation that it subsequently acts upon. I consider the respects in which both of these claims sound non-Darwinian, even though they have long been understood by supporters and critics alike to be virtually constitutive of Darwinism. (shrink)

Two strategies for using a model as “null” are distinguished. Null modeling evaluates whether a process is causally responsible for a pattern by testing it against a null model. Baseline modeling measures the relative significance of various processes responsible for a pattern by detecting deviations from a baseline model. When these strategies are conflated, models are illegitimately privileged as accepted until rejected. I illustrate this using the neutral theory of ecology and draw general lessons from this case. First, scientists cannot (...) draw certain conclusions using null modeling. Second, these conclusions follow using baseline modeling, but doing so requires more evidence. (shrink)

Among philosophers of science, there is now a widespread agreement that the DN model of explanation is poorly equipped to account for explanations in biology. Rather than identifying laws, so the consensus goes, researchers explain biological capacities by constructing a model of the underlying mechanism.We think that the dichotomy between DN explanations and mechanistic explanations is misleading. In this article, we argue that there are cases in which biological capacities are explained without constructing a model of the underlying mechanism. Although (...) these explanations do not conform to Hempel’s DN model, they do invoke more or less stable generalisations. Because they invoke generalisations and have the form of an argument, we call them inferential explanations. We support this claim by considering two examples of explanations of biological capacities: pigeon navigation and photoperiodism. Next, we will argue that these non-mechanistic explanations are crucial to biology in three ways: sometimes, they are the only thing we have, they are heuristically useful, and they provide genuine understanding and so are interesting in their own right.In the last sections we discuss the relation between types of explanations and types of experiments and situate our views within some relevant debates on explanatory power and explanatory virtues. (shrink)

Today, mechanisms and mechanistic explanation are very popular in philosophy of science and are deemed a welcome alternative to laws of nature and deductive‐nomological explanation. Starting from Mitchell's pragmatic notion of laws, I cast doubt on their status as a genuine alternative. I argue that (1) all complex‐systems mechanisms ontologically must rely on stable regularities, while (2) the reverse need not hold. Analogously, (3) models of mechanisms must incorporate pragmatic laws, while (4) such laws themselves need not always refer to (...) underlying mechanisms. Finally, I show that Mitchell's account is more encompassing than the mechanistic account *Received August 2008; revised January 2010. †To contact the author, please write to: Centre for Logic and Philosophy of Science, Ghent University, Blandijnberg 2, B‐9000 Belgium; e‐mail: [email protected]. (shrink)

Until recently, the notions of function and multiple realization were supposed to save the autonomy of psychological explanations. Furthermore, the concept of supervenience presumably allows both dependence of mind on brain and non-reducibility of mind to brain, reconciling materialism with an independent explanatory role for mental and functional concepts and explanations. Eliminativism is often seen as the main or only alternative to such autonomy. It gladly accepts abandoning or thoroughly reconstructing the psychological level, and considers reduction if successful as equivalent (...) with elimination. In comparison with the philosophy of mind, the philosophy of biology has developed more subtle and complex ideas about functions, laws, and reductive explanation than the stark dichotomy of autonomy or elimination. It has been argued that biology is a patchwork of local laws, each with different explanatory interests and more or less limited scope. This points to a pluralistic, domain-specific and multi-level view of explanations in biology. Explanatory pluralism has been proposed as an alternative to eliminativism on the one hand and methodological dualism on the other hand. It holds that theories at different levels of description, like psychology and neuroscience, can co-evolve, and mutually influence each other, without the higher-level theory being replaced by, or reduced to, the lower-level one. Such ideas seem to tally with the pluralistic character of biological explanation. In biological psychology, explanatory pluralism would lead us to expect many local and non-reductive interactions between biological, neurophysiological, psychological and evolutionary explanations of mind and behavior. This idea is illustrated by an example from behavioral genetics, where genetics, physiology and psychology constitute distinct but interrelated levels of explanation. Accounting for such a complex patchwork of related explanations seems to require a more sophisticated and precise way of looking at levels than the existing ideas on (reductive and non-reductive) explanation in the philosophy of mind. (shrink)

Recent discussion of mechanism has suggested new approaches to several issues in the philosophy of science, including theory structure, causal explanation, and reductionism. Here, I apply what I take to be the fruits of the 'new mechanical philosophy' to an analysis of a contemporary debate in evolutionary biology about the role of natural selection in speciation. Traditional accounts of that debate focus on the geographic context of genetic divergence--namely, whether divergence in the absence of geographic isolation is possible (or significant). (...) Those accounts are at best incomplete, I argue, because they ignore the mechanisms producing divergence and miss what is at stake in the biological debate. I argue that the biological debate instead concerns the scope of particular speciation mechanisms which assign different roles to natural selection at various stages of divergence. The upshot is a new interpretation of the crux of that debate--namely, whether divergence with gene flow is possible (or significant) and whether the isolating mechanisms producing it are adaptive. (shrink)

The purpose of this essay is to present and analyse the basic assumptions of Leszek Nowak’s conception of the unity of science. According to Nowak, the unity of science is manifested in the common application of the method of idealisation in scientific research. In accordance with his conception, regardless of the discipline they represent, researchers go through the same stages in building a theory. Two key ones among them are: introducing idealising assumptions into the representation and then their concretisation. In (...) this view, idealisation is the basis of the scientific method, while other cognitive procedures complement it. Nowak’s conception has particular relevance in the context of the dispute between naturalism and anti-naturalism and in the context of the continuing rift between social scientists and natural scientists. It calls into question the anti-naturalist thesis of the ontological uniqueness of social sciences and the resulting methodological consequences. I argue that Nowak’s conception is a cognitively valuable contribution to the contemporary epistemology of science, but it also has weaknesses, mainly due to the limitations of applying the idealisation-concretisation scheme in research practice. For it turns out, as I point out in this essay, that many idealising assumptions are not subject to concretisation and that concretisations do not always condition an increase in the explanatory and/or predictive power of the representations. (shrink)

The evolution of sexual reproduction is a striking case of explanatory pluralism, meaning that one needs to refer to more than one explanation in order to adequately account for it. I develop the concept a domain of phenomena in order to analysis this pluralism. Pluralism exists when a phenomenon can be included in more that one homogeneous domain or in a heterogeneous domain. I argue that in some cases domain partitioning can be used to decrease pluralism, but that in the (...) case of sex domains are overlapping and interconnecting, or in other words bear an orthogonal relationship to one another, and hence cannot be partitioned in such a way as to eliminate pluralism. (shrink)

The current assumptions of knowledge acquisition brought about the crisis in the reproducibility of experiments. A complementary perspective should account for the specific causality characteristic of life by integrating past, present, and future. A “second Cartesian revolution,” informed by and in awareness of anticipatory processes, should result in scientific methods that transcend the theology of determinism and reductionism. In our days, science, itself an expression of anticipatory activity, makes possible alternative understandings of reality and its dynamics. For this purpose, the (...) study advances G-complexity for defining and comparing decidable and undecidable knowledge. AI and related computational expressions of knowledge could benefit from the awareness of what distinguishes the dynamics of life from any other expressions of change. (shrink)

In this paper, I discuss the problem of scientific laws in general and laws of biology in particular. After reviewing the debate around the existence of laws in biology, I examine the subject in the light of the structuralist notion of a fundamental law and argue for the law of matching as the fundamental law of genetics.

A variety of different arguments have been offered for teaching ‘‘both sides’’ of the evolution/ID debate in public schools. This article reviews five of the most common types of arguments advanced by proponents of Intelligent Design and demonstrates how and why they are founded on confusion and misunderstanding. It argues on behalf of teaching evolution, and relegating discussion of ID to philosophy or history courses.

The evolution of sexual reproduction is a case of explanatory pluralism, meaning that there is more than one explanation for this phenomenon. I use the concept of a domain to more clearly explicate the various explananda that can be found in this case. I argue that although pluralism with respect to some types of domains can be decreased using van Fraassen's pragmatics of explanation, there remains an important class of domain, an orthogonal domain, for which this is not the case.

This paper develops a critical response to John Beatty’s recent (2006) engagement with Stephen Jay Gould’s claim that evolutionary history is contingent. Beatty identifies two senses of contingency in Gould’s work: an unpredictability sense and a causal dependence sense. He denies that Gould associates contingency with stochastic phenomena, such as drift. In reply to Beatty, this paper develops two main claims. The first is an interpretive claim: Gould really thinks of contingency has having to do with stochastic effects at the (...) level of macroevolution, and in particular with unbiased species sorting. This notion of contingency as macro-level stochasticity incorporates both the causal dependence and the unpredictability senses of contingency. The second claim is more substantive: Recent attempts by other scientists to put Gould’s claim to the test fail to engage with the hypothesis that species sorting sometimes resembles a lottery. Gould’s claim that random sorting is a significant macroevolutionary phenomenon remains an intriguing and largely untested live hypothesis about evolution. (shrink)

The primary purpose of this paper is to argue that biologists should stop citing Karl Popper on what a genuinely scientific theory is. Various ways in which biologists cite Popper on this matter are surveyed, including the use of Popper to settle debates on methodology in phylogenetic systematics. It is then argued that the received view on Popper—namely, that a genuinely scientific theory is an empirically falsifiable one—is seriously mistaken, that Popper’s real view was that genuinely scientific theories have the (...) form of statements of laws of nature. It is then argued that biology arguably has no genuine laws of its own. In place of Popperian falsifiability, it is suggested that a cluster class epistemic values approach (which subsumes empirical falsifiability) is the best solution to the demarcation problem between genuine science and pseudo- or non-science. (shrink)

We evaluate a common reasoning strategy used in community ecology and comparative psychology for selecting between competing hypotheses. This strategy labels one hypothesis as a “null” on the grounds of its simplicity and epistemically privileges it as accepted until rejected. We argue that this strategy is unjustified. The asymmetrical treatment of statistical null hypotheses is justified through the experimental and mathematical contexts in which they are used, but these contexts are missing in the case of the “pseudo-null hypotheses” found in (...) our case studies. Moreover, statistical nulls are often not epistemically privileged in practice over their alternatives because failing to reject the null is usually a negative result about the alternative, experimental hypothesis. Scientists should eschew the appeal to pseudo-nulls. It is a rhetorical strategy that glosses over a commitment to valuing simplicity over other epistemic virtues in the name of good scientific and statistical methodology. (shrink)