This paper analyzes two ways idealized biological models produce factive scientific understanding. I then argue that models can provide factive scientific understanding of a phenomenon without providing an accurate representation of the features of their real-world target system. My analysis of these cases also suggests that the debate over scientific realism needs to investigate the factive scientific understanding produced by scientists’ use of idealized models rather than the accuracy of scientific models themselves.

The taxa that appear in biological classifications are commonly seen as representing information about the traits of their member organisms. This paper examines in what way taxa feature in the storage and retrieval of such information. I will argue that taxa do not actually store much information about the traits of their member organisms. Rather, I want to suggest, taxa should be understood as functioning to localize organisms in the genealogical network of life on Earth. Taxa store information about where (...) organisms are localized in the network, which is important background information when it comes to establishing knowledge about organismal traits, but it is not itself information about these traits. The view of species and higher taxa that is proposed here follows from examining three problems that occur in contemporary biological systematics and are discussed here: the problem of generalization over taxa, the problem of phylogenetic inference, and the problematic nature of the Tree of Life. (shrink)

The taxa that appear in biological classifications are commonly seen as representing information about the traits of their member organisms. This paper examines in what way taxa feature in the storage and retrieval of such information. I will argue that taxa do not actually store much information about the traits of their member organisms. Rather, I want to suggest, taxa should be understood as functioning to localize organisms in the genealogical network of life on Earth. Taxa store information about where (...) organisms are localized in the network, which is important background information when it comes to establishing knowledge about organismal traits, but it is not itself information about these traits. The view of species and higher taxa that is proposed here follows from examining three problems that occur in contemporary biological systematics and are discussed here: the problem of generalization over taxa, the problem of phylogenetic inference, and the problematic nature of the Tree of Life. (shrink)

Real kinds, both natural and social categories, are characterized by rich inductive potential. They have relatively stable sets of conceptually independent projectable properties. Somewhat surprisingly, even some purely social categories show such multiple projectability. The article explores the origin of the inductive richness of social categories and concepts. I argue that existing philosophical accounts provide only a partial explanation, and mechanisms of boundary formation and stabilization must be brought into view for a more comprehensive account of inductively rich social categories.

Many scientific models in biology are how-possibly models. These models depict things as they could be, but do not necessarily capture actual states of affairs in the biological world. In contemporary philosophy of science, it is customary to treat how-possibly models as second-rate theoretical tools. Although possibly important in the early stages of theorizing, they do not constitute the main aim of modelling, namely, to discover the actual mechanism responsible for the phenomenon under study. In the paper it is argued (...) that this prevailing picture does not do justice to the synthetic strategy that is commonly used in biological engineering. In synthetic biology, how-possibly models are not simply speculations or eliminable scaffolds towards a single how-actually model, but indispensable design hypotheses for a field whose ultimate goal is to build novel biological systems. The paper explicates this by providing an example from the study of alternative genetic systems by synthetic biologist Steven Benner and his group. The case will also highlight how the method of synthesis, even when it fails, provides an effective way to limit the space of possible models for biological systems. (shrink)

The concept of hierarchical organization is commonplace in science. Subatomic particles compose atoms, which compose molecules; cells compose tissues, which compose organs, which compose organisms; etc. Hierarchical organization is particularly prominent in ecology, a field of research explicitly arranged around levels of ecological organization. The concept of levels of organization is also central to a variety of debates in philosophy of science. Yet many difficulties plague the concept of discrete hierarchical levels. In this paper, we show how these difficulties undermine (...) various implications ascribed to hierarchical organization, and we suggest the concept of scale as a promising alternative to levels. Investigating causal processes at different scales offers a way to retain a notion of quasi-levels that avoids the difficulties inherent in the classic concept of hierarchical levels of organization. Throughout, our focus is on ecology, but the results generalize to other invocations of hierarchy in science and philosophy of science. (shrink)

Cancer is typically spoken of as a “complex” disease. But, in what sense are cancers “complex”? Is there one sense, or several? What implications does this complexity have – both for how we study, and how we intervene upon cancers? The aim of this paper is first, to clarify the variety of senses in which cancer is spoken of as "complex" in the scientific literature, and second, to discover what explanatory and predictive roles such features play.

My aim in this paper is to articulate an account of scientific modeling that reconciles pluralism about modeling with a modest form of scientific realism. The central claim of this approach is that the models of a given physical phenomenon can present different aspects of the phenomenon. This allows us, in certain special circumstances, to be confident that we are capturing genuine features of the world, even when our modeling occurs independently of a wholly theoretical motivation. This framework is illustrated (...) using a recent debate from meteorology. (shrink)

The Nagel inspired “something-it-is-like” conception of conscious experience remains a dominant approach in philosophy. In this paper I criticize a prevalent philosophical construal of SIL consciousness, one that understands SIL as a property of mental states rather than entities as a whole. I argue against thinking of SIL as a property of states, showing how such a view is in fact prevalent, under-warranted, and philosophically pernicious in that it often leads to an implausible reduction of conscious experience to qualia. I (...) then develop a holistic conception of SIL for entities and argue that it has at least equal pre-empirical warrant, is more conservative philosophically in that it decides less from the a priori “armchair,” and enjoys a fruitful two-way relationship with empirical work. (shrink)

The Nagel inspired “something-it-is-like” conception of conscious experience remains a dominant approach in philosophy. In this paper I criticize a prevalent philosophical construal of SIL consciousness, one that understands SIL as a property of mental states rather than entities as a whole. I argue against thinking of SIL as a property of states, showing how such a view is in fact prevalent, under-warranted, and philosophically pernicious in that it often leads to an implausible reduction of conscious experience to qualia. I (...) then develop a holistic conception of SIL for entities and argue that it has at least equal pre-empirical warrant, is more conservative philosophically in that it decides less from the a priori “armchair,” and enjoys a fruitful two-way relationship with empirical work. (shrink)

Philosophers of science have often favoured reductive approaches to how-possibly explanation. This article identifies three alternative conceptions making how-possibly explanation an interesting phenomenon in its own right. The first variety approaches “how possibly X?” by showing that X is not epistemically impossible. This can sometimes be achieved by removing misunderstandings concerning the implications of one’s current belief system but involves characteristically a modification of this belief system so that acceptance of X does not result in contradiction. The second variety offers (...) a potential how-explanation of X. It is usually followed by a range of further potential how-explanations of the same phenomenon. In recent literature the factual claims implied by the second variety have been downplayed whereas the heuristic role of mapping the space of conceptual possibilities has been emphasized. I will focus especially on this truth-bracketing sense of potentiality when looking closer at the second variety in the paper. The third variety has attracted less interest. It presents a partial how-explanation of X. Typically it aims to establish the existence of a mechanism by which X could be and was generated. The third conception stands out as the natural alternative for the advocate of ontic how-possibly explanations. This article transfers Salmon’s view that explanation-concepts can be broadly divided into epistemic, modal, and ontic to the context of how-possibly explanations. Moreover, it is argued that each of the three above-mentioned varieties of how-possibly explanation occurs in science. To recognize this may be especially relevant for philosophers. We are often misled by the promises of various why-explanation accounts, and seem to have forgotten nearly everything about the diversity of how-possibly explanations. (shrink)

This paper defends the viability of de-idealization strategies in economic modeling against recent criticism. De-idealization occurs when an idealized assumption of a theoretical model is replaced with a more realistic one. Recently, some scholars have raised objections against the possibility or fruitfulness of de-idealizing economic models, suggesting that economists do not employ this kind of strategy. We present a detailed case study from the theory of industrial organization, discussing three different models, two of which can be construed as de-idealized versions (...) of the first. We conclude that recent pessimism about de-idealization in economics is largely unfounded, and that de-idealization strategies are not only possible but also widely employed in economics. (shrink)

Multiple biological groups, such as ant colonies, appear to have a noteworthy inefficiency: they contain vast amounts of redundant members that are not strictly needed to maintain the group. Philosophers and biologists have proposed that such inefficiency is illusory because redundancy enhances the resilience of groups when living under harsh conditions. Still, this proposal is unsatisfactory in different respects. First, it is too vague to account for when redundancy is selectively advantageous. Furthermore, it overlooks cases in which redundancy fails to (...) increase the resilience of groups. This paper offers an account of group redundancy that addresses these difficulties. Specifically, it advances the hypothesis that the mere presence of harsh conditions is not what drives the evolution of redundancy; rather, it is the fact organisms are often unable to predict when they will face harsh conditions. Redundancy enables groups to properly respond to unpredictable circumstances without resorting to the unreliable detection systems of their members. A better understanding of the phenomenon of redundancy is likely to impact other key issues in philosophy of science, including the evolution of cooperation and transitions in individuality, and the role of redundancy in complex systems, be they biological or not. (shrink)

Early 20th century philosopher Henri Bergson posited an initial push that propelled the diversity of life forward into a varied, novel future: The élan vital, a necessary force or impulse that animated life’s progress and development. His idea had largely been abandoned by mid-century. Even so, much of the conceptual and explanatory work this impulse targeted is yet in want of an explanation. In particular, Bergson’s derelict ideas on evolution addressed three areas that have once again become relevant in the (...) effort to unite evolutionary genetics, biological development, and ecological context : the purposeful nature of individual organisms and their parts; the integrative, holistic, non-linear emergent dynamics seen in evolutionary processes; and how genuine novelty emerges into the universe :422, 2016; Simondon et al. in On the mode of existence of technical objects. Univocal series, Univocal Publishing LLC, Minneapolis, 2017; Bang, in: Winther-Lindqvist, Bang, Valsiner Nothingness: philosophical insights into psychology, Transaction Publishers, Somerset, 2016; Moreno and Mossio in Biological autonomy: a philosophical and theoretical enquiry. History, philosophy and theory of the life sciences, Springer, Dordrecht, 2015). In this paper I argue that Bergson’s ideas may yet be relevant to these questions, and his work warrants a reexamination in light of current problems in evolutionary biology. This is not a call to ‘return’ to Bergson, nevertheless his notions about complexity suggest ways of looking at current biological problems in ways that offer a heuristic insight worth entertaining. Bergson’s Nobel Prize-winning book, Creative Evolution, provided a strikingly prescient early 20th century framework for understanding how Darwinian evolution acts as an engine for generating new forms, University Press of America, Lanham, Bergson 1911). (shrink)

Synthetic biology is an umbrella term that covers a range of aims, approaches, and techniques. They are all brought together by common practices of analogizing, synthesizing, mechanicizing, and kludging. With a focus on kludging as the connection point between biology, engineering, and evolution, I show how synthetic biology’s successes depend on custom-built kludges and a creative, “make-it-work” attitude to the construction of biological systems. Such practices do not fit neatly, however, into synthetic biology’s celebration of rational design. Nor do they (...) straightforwardly embody Richard Feynman’s “last blackboard” statement that without creating something it cannot be understood. Reflecting further on the relationship between synthetic construction and knowledge making gives philosophy of science new avenues of insight into scientific practice. (shrink)

Multilevel research strategies characterize contemporary molecular inquiry into biological systems. We outline conceptual, methodological, and explanatory dimensions of these multilevel strategies in microbial ecology, systems biology, protein research, and developmental biology. This review of emerging lines of inquiry in these fields suggests that multilevel research in molecular life sciences has significant implications for philosophical understandings of explanation, modeling, and representation.

Although the literature on the issue of pluralism within the philosophy of science is very extensive, this paper focuses on the metaphysical causal pluralism that emerges from the new mechanistic discussion on causality. The main aim is to situate the new mechanistic views on causation within the account of varieties of causal pluralism framed by Psillos ( 2009 ). Paying attention to his taxonomy of metaphysical views on causation (i.e., the straightjacket view, the functional view, the two-concept view, the agnostic (...) view and the atheist view) will help clarify differences in opinion and, at the same time, make it possible to elucidate the main metaphysical theses present within the new mechanistic debate. Special attention is given to S. Glennan’s theory of causation, since it is unique in offering an overall metaphysical view of the issue. It is also argued that mechanists are not “atheists” on causation: while all of them are causal realists, most mechanists are “agnostic” on causation, with a few exceptions such as S. Glennan, P. Machamer and J. Bogen. (shrink)

The realities of human agency and decision making pose serious challenges for research ethics. This article explores six major challenges that require more attention in the ethics education of students and scientists and in the research on ethical conduct in science. The first of them is the routinization of action, which makes the detection of ethical issues difficult. The social governance of action creates ethical problems related to power. The heuristic nature of human decision making implies the risk of ethical (...) bias. The moral disengagement mechanisms represent a human tendency to evade personal responsibility. The greatest challenge of all might be the situational variation in people’s ethical behaviour. Even minor situational factors have a surprisingly strong influence on our actions. Furthermore, finally, the nature of ethics itself also causes problems: instead of clear answers, we receive a multitude of theories and intuitions that may sometimes be contradictory. All these features of action and ethics represent significant risks for ethical conduct in science. I claim that they have to be managed within the everyday practices of science and addressed explicitly in research ethics education. I analyse them and suggest some ways in which their risks can be alleviated. (shrink)

The feeling of clarity can be dangerously seductive. It is the feeling associated with understanding things. And we use that feeling, in the rough-and-tumble of daily life, as a signal that we have investigated a matter sufficiently. The sense of clarity functions as a thought-terminating heuristic. In that case, our use of clarity creates significant cognitive vulnerability, which hostile forces can try to exploit. If an epistemic manipulator can imbue a belief system with an exaggerated sense of clarity, then they (...) can induce us to terminate our inquiries too early — before we spot the flaws in the system. How might the sense of clarity be faked? Let’s first consider the object of imitation: genuine understanding. Genuine understanding grants cognitive facility. When we understand something, we categorize its aspects more easily; we see more connections between its disparate elements; we can generate new explanations; and we can communicate our understanding. In order to encourage us to accept a system of thought, then, an epistemic manipulator will want the system to provide its users with an exaggerated sensation of cognitive facility. The system should provide its users with the feeling that they can easily and powerfully create categorizations, generate explanations, and communicate their understanding. And manipulators have a significant advantage in imbuing their systems with a pleasurable sense of clarity, since they are freed from the burdens of accuracy and reliability. I offer two case studies of seductively clear systems: conspiracy theories; and the standardized, quantified value systems of bureaucracies. (shrink)

In this paper, I show how idealizations contribute to social activities in science, such as the recruitment of experts to a research project. These contributions have not been explicitly discussed by recent philosophical accounts of scientific idealization. These accounts have focused on how idealizations influence activities like scientific theorization, explanation, and modeling. Other accounts focus on how idealizations influence policy-making and science communication. I expand these accounts by exploring the uses of idealized phylogenetic trees in science. Trees are not only (...) useful for improving our understanding and public communication of evolutionary history, but they also help with the organization of laboratories and collaboration among scientists. Attending to the relation between idealizations and these social practices in science matters. It can help us understand why idealized models become entrenched and why certain social practices change over time. (shrink)

In this paper I argue that many scholars involved in the contemporary free will debates have underappreciated the philosophical appeal of agent causation because the resources of contemporary emergentism have not been adequately introduced into the discussion. Whereas I agree that agent causation’s main problem has to do with its intelligibility, particularly with respect to the issue of how substances can be causally relevant, I argue that the notion of substance causation can be clearly articulated from an emergentist framework. According (...) to my proposal, a free agent is _a causally powerful substance that emerges in an anomic way from her constitutive mental events_, downwardly constraining, selecting and, in this way, having control on them. As we shall see, this particular concept of agent causation not only makes sense of the deep insight behind agent libertarianism, but it also provides us with the resources to solve some of the main objections that have been raised against it. It is true that here I cannot develop a complete defense of the evidential credentials of emergentism. Still, even if the considerations that follow do not serve to convince detractors of agent causal libertarian accounts of free will, they do suggest that libertarian agent causation is more promising than is typically acknowledged. (shrink)

This paper argues that a plant together with the symbiotic fungus attached to its roots, a mycorrhizal collective, is an evolutionary individual, and further, that mycorrhizal individuality has important implications for evolutionary theory. Theoretical individuation is defended and then employed to show that mycorrhizal collectives function as interactors according to David Hull’s replicator-interactor model of evolution by natural selection, and because they have the potential to engage in pseudo-vertical transmission, mycorrhizal collectives also function as Darwinian individuals, according to Peter Godfrey-Smith’s (...) Darwinian Populations model of evolution by natural selection. Mycorrhizae in nature usually connect the roots of multiple plants, so mycorrhizal individuality entails the existence of overlapping evolutionary individuals, and because the potential to engage in pseudo-vertical transmission comes in degrees, it follows that these overlapping evolutionary individuals also come in degrees. I suggest here that the degree of evolutionary individuality in a symbiotic collective corresponds to its probability of reproducing with vertical or pseudo-vertical transmission. This probability constitutes a fourth parameter of graded Darwinian individuality in collective reproducers and warrants an update to Godfrey-Smith’s 3D model. (shrink)

Philosophers are approaching a consensus that biological individuality, including evolutionary individuality, comes in degrees. Graded evolutionary individuality presents a puzzle when juxtaposed with another widely embraced view: that evolutionary individuality follows from being a selectable member of a Darwinian population. Population membership is, on the orthodox view, a bivalent condition, so how can members of Darwinian populations vary in their degree of individuality? This article offers a solution to the puzzle, by locating difference in degree of evolutionary individuality at the (...) level of population lineages, some of which are more Darwinian than others. In doing so, it sheds light on graded individuality in overlapping and nested population lineages, such as those that arise in multilevel selection and symbiotic collectives. (shrink)

Reference models of the earth’s interior play an important role in the acquisition of knowledge about the earth’s interior and the earth as a whole. Such models are used as a sort of standard reference against which data are compared. I argue that the use of reference models merits more attention than it has gotten so far in the literature on models, for it is an example of a method of doing science that has a long and significant history, and (...) a study of reference models could increase our understanding of this methodology. (shrink)

Philosophical accounts of emergence have been explicated in terms of logical relationships between statements (derivation) or static properties (function and realization). Jaegwon Kim is a modern proponent. A property is emergent if it is not explainable by (or reducible to) the properties of lower level components. This approach, I will argue, is unable to make sense of the kinds of emergence that are widespread in scientific explanations of complex systems. The standard philosophical notion of emergence posits the wrong dichotomies, confuses (...) compositional physicalism with explanatory physicalism, and is unable to represent the type of dynamic processes (self-organizing feedback) that both generate emergent properties and express downward causation. (shrink)

I analyze the epistemic strategies used by paleontologists (between 1830–1930) to reconstruct features of ancient organisms from fossilized bodies and footprints by presenting two heuristics: (1) a “claim of harmony” which posits the harmonious interaction of natural objects in order for complex systems to be simplified and (2) the “kintsugi heuristic” which is used inter-theoretically to explore new claims of harmony. I apply these to three successive historical cases: Georges Cuvier’s laws of correlation, the panpsychist paleontology of Edward Drinker Cope, (...) and the single-character approach of Henry Fairfield Osborn. (shrink)

Is there a field of social intelligence? Many various disciplines approach the subject and it may only seem natural to suppose that different fields of study aim at explaining different phenomena; in other words, there is no special field of study of social intelligence. In this paper, I argue for an opposite claim. Namely, there is a way to integrate research on social intelligence, as long as one accepts the mechanistic account to explanation. Mechanistic integration of different explanations, however, comes (...) at a cost: mechanism requires explanatory models to be fairly complete and realistic, and this does not seem to be the case for many models concerning social intelligence, especially models of economical behavior. Such models need either be made more realistic, or they would not count as contributing to the same field. I stress that the focus on integration does not lead to ruthless reductionism; on the contrary, mechanistic explanations are best understood as explanatorily pluralistic. (shrink)

Is there a field of social intelligence? Many various disciplines approach the subject and it may only seem natural to suppose that different fields of study aim at explaining different phenomena; in other words, there is no special field of study of social intelligence. In this paper, I argue for an opposite claim. Namely, there is a way to integrate research on social intelligence, as long as one accepts the mechanistic account to explanation. Mechanistic integration of different explanations, however, comes (...) at a cost: mechanism requires explanatory models to be fairly complete and realistic, and this does not seem to be the case for many models concerning social intelligence, especially models of economical behavior. Such models need either be made more realistic, or they would not count as contributing to the same field. I stress that the focus on integration does not lead to ruthless reductionism; on the contrary, mechanistic explanations are best understood as explanatorily pluralistic. (shrink)

The claim defended in the paper is that the mechanistic account of explanation can easily embrace idealization in big-scale brain simulations, and that only causally relevant detail should be present in explanatory models. The claim is illustrated with two methodologically different models: Blue Brain, used for particular simulations of the cortical column in hybrid models, and Eliasmith’s SPAUN model that is both biologically realistic and able to explain eight different tasks. By drawing on the mechanistic theory of computational explanation, I (...) argue that large-scale simulations require that the explanandum phenomenon is identified; otherwise, the explanatory value of such explanations is difficult to establish, and testing the model empirically by comparing its behavior with the explanandum remains practically impossible. The completeness of the explanation, and hence of the explanatory value of the explanatory model, is to be assessed vis-à-vis the explanandum phenomenon, which is not to be conflated with raw observational data and may be idealized. I argue that idealizations, which include building models of a single phenomenon displayed by multi-functional mechanisms, lumping together multiple factors in a single causal variable, simplifying the causal structure of the mechanisms, and multi-model integration, are indispensable for complex systems such as brains; otherwise, the model may be as complex as the explanandum phenomenon, which would make it prone to so-called Bonini paradox. I conclude by enumerating dimensions of empirical validation of explanatory models according to new mechanism, which are given in a form of a “checklist” for a modeler. (shrink)

One of the critical issues in the philosophy of science is to understand scientific knowledge. This paper proposes a novel approach to the study of reflection on science, called “cognitive metascience”. In particular, it offers a new understanding of scientific knowledge as constituted by various kinds of scientific representations, framed as cognitive artifacts. It introduces a novel functional taxonomy of cognitive artifacts prevalent in scientific practice, covering a huge diversity of their formats, vehicles, and functions. As a consequence, toolboxes, conceptual (...) frameworks, theories, models, and individual hypotheses can be understood as artifacts supporting our cognitive performance. It is also shown that by empirically studying how artifacts function, we may discover hitherto undiscussed virtues and vices of these scientific representations. This paper relies on the use of language technology to analyze scientific discourse empirically, which allows us to uncover the metascientific views of researchers. This, in turn, can become part of normative considerations concerning virtues and vices of cognitive artifacts. (shrink)

It is wholly uncontroversial that measurements-or, more properly, propositions that are measurement reports-are often paradigmatically good cases of propositions that serve the function of evidence. In normal cases it is also obvious that stating such a report is an utterly pedestrian case of successful assertion. So, for example, there is nothing controversial about the following claims: (1) that a proposition to the effect that a particular thermometer reads 104C when properly used to determine the temperature of a particular patient is (...) evidence that the patient in question has a fever and (2) that there is nothing wrong with asserting the proposition that a particular thermometer reads 104C for appropriate reasons of communication, etc. when the thermometer has been properly used to determine the temperature of a particular patient. Here it will be shown that Timothy Williamson’s commitments to a number of principles about knowledge and assertion imply that a whole class of utterly ordinary statements like these that are used as evidence are not really evidence because they are not knowledge and so are (perversely) unassertable according to his principled commitments. This paper deals primarily with the second of these two problems and an alternative account of the norms of assertion is introduced which allows for the assertability of such measurement reports. (shrink)

Interactionism holds that explanatory and interpretive projects are mutually enriching. If so, then the evolutionary and cognitive science of religions’ explanatory theories should aid interpretive projects concerning religious meaning. Although interpretive accounts typically focus on the local and the particular, interpreters over the past century have construed Freud and Marx as offering general interpretive theories. So, precedent for general interpretive theorizing exists. 4E cognitive science, which champions how cognition is embedded in natural and cultural settings, extended into external structures, enacted (...) via motor routines, and embodied via representations rooted in human bodily form, has encouraged interpretive researchers. Theories of embodied cognition especially have embraced a sweeping view of meaning that attends to the emotions’ role and to their evolutionary origins. That inspires a 6E cognitive science that attends to the emotional and evolved dimensions of cognition too and opens up the possibility of general interpretive theories of broadly Darwinian character. Evolved cognitive systems qualify as maturationally natural cognition, which exhibits a distinctive constellation of features. The by-product theory holds that religious representations’ engagement of maturationally natural cognition fosters religions’ success. Representations with some minimal violation of intuitive expectations concerning some ontological category grab attention, stick in memory, and preserve the many automatic inferences accompanying the category. The empirical evidence for this and other elaborations of the by-product view suggests that it discloses dynamics of evolved cognition and associated emotions that tend to guide the pursuit of religious meanings systematically toward well-worn grooves in the semantic landscape. (shrink)

In recent years, quite a few evolutionary psychologists have come to embrace a heuristic interpretation of the discipline. They claim that, no matter how methodologically incomplete, adaptive thinking works fine as a good heuristic that effectively reduces the hypothesis space by generating novel and promising hypotheses that can eventually be empirically tested. The purpose of this article is to elucidate the use of heuristics in evolutionary psychology, thereby clarifying the role adaptive thinking has to play. To that end, two typical (...) heuristic interpretations—Machery’s "bootstrap strategy" and Goldfinch’s heuristically streamlined evolutionary psychology—are examined, focusing on the relationship between adaptive thinking and heuristics. The article draws two primary conclusions. The first is that the reliability of the heuristic hypothesis generation procedure should count no less than the conclusiveness of the final testing procedure in establishing scientific facts; nature does not always get the last word. Philosophy also counts. The second is that adaptive thinking constitutes a core heuristic in evolutionary psychology that provides the discipline with its raison d'être, but this is only possible when adaptive thinking is substantiated with sufficient historical underpinnings. (shrink)

In this article, we analyse how researchers use the categories of race and ethnicity with reference to genetics and genomics. We show that there is still considerable conceptual “messiness” (despite the wide-ranging and popular debate on the subject) when it comes to the use of ethnoracial categories in genetics and genomics that among other things makes it difficult to properly compare and interpret research using ethnoracial categories, as well as draw conclusions from them. Finally, we briefly reconstruct some of the (...) biases of reductionism to which geneticists (as well as other researchers referring to genetic methods and explanations) are particularly exposed to, and we analyse the problem in the context of the biologization of ethnoracial categories. Our work constitutes a novel, in-depth contribution to the debate about reporting race and ethnicity in biomedical and health research. First, we reconstruct the theoretical background assumptions about racial ontology which researchers implicitly presume in their studies with the aid of a sample of recent papers published in medical journals about COVID-19. Secondly, we use the typology of the biases of reductionism to the problem of biologization of ethnoracial categories with reference to genetics and genomics. (shrink)

Modelers are tackling ever more complex systems with the aid of computation. Model-based inferences can play a key role in their ability to handle complexity and produce reliable or informative models. We study here the role of model-based inference in the modern field of computational systems biology. We illustrate how these inferences operate and analyze the material and theoretical bases or conditions underlying their effectiveness. Our investigation reiterates the significance and centrality of model-based reasoning in day-to-day problem-solving practices, and the (...) role that debugging processes of partial or incomplete models can play in scientific inference and scientific discovery, particularly with respect to complex systems. We present several deeper implications such an analysis has for philosophy of science regarding the role of models in scientific practice. (shrink)

Modern integrative systems biology defines itself by the complexity of the problems it takes on through computational modeling and simulation. However in integrative systems biology computers do not solve problems alone. Problem solving depends as ever on human cognitive resources. Current philosophical accounts hint at their importance, but it remains to be understood what roles human cognition plays in computational modeling. In this paper we focus on practices through which modelers in systems biology use computational simulation and other tools to (...) handle the cognitive complexity of their modeling problems so as to be able to make significant contributions to understanding, intervening in, and controlling complex biological systems. We thus show how cognition, especially processes of simulative mental modeling, is implicated centrally in processes of model-building. At the same time we suggest how the representational choices of what to model in systems biology are limited or constrained as a result. Such constraints help us both understand and rationalize the restricted form that problem solving takes in the field and why its results do not always measure up to expectations. (shrink)

Many philosophers of science think scientific practice can benefit from philosophical concepts, and as such philosophy of science should play a direct role in science and engineering education. In this paper we consider a highly integrative course design strategy for integrating philosophy of science in specific disciplinary educational programmes through adaptation, operationalization and embedding of philosophy of science material to fit both the scientific and educational structure of a programme. The goal of the strategy is to help encourage students to (...) recognize the value of philosophical concepts to scientific decision making and to apply them in their own scientific practice. We use the example of a 7.5 ECTS civil engineering course which implements this design at a European technical university, to elaborate these concepts, and present some evidence on how students receive the course. We discuss some of challenges and limitations of implementing this kind of strategy for teaching philosophy of science. (shrink)

Prediction and control sufficient for reliable medical and other interventions are prominent aims of modeling in systems biology. The short-term attainment of these goals has played a strong role in projecting the importance and value of the field. In this paper I identify the standard models must meet to achieve these objectives as predictive robustness—predictive reliability over large domains. Drawing on the results of an ethnographic investigation and various studies in the systems biology literature, I explore four current obstacles to (...) achieving predictive robustness; data constraints, parameter uncertainty, collaborative constraints and system-scale requirements. I use a case study and the commentary of systems biologists themselves to show that current practices in the field, rather than pursuing these goals, frequently use models heuristically to investigate and build understanding of biological systems that do not meet standards of predictive robustness but are nonetheless effective uses of computation. A more heuristic conception of modeling allows us to interpret current practices as ways that manage these obstacles more effectively, particularly collaborative constraints, such that modelers can in the long-run at least work towards prediction and control. (shrink)

In this paper, I present a new framework supporting the claim that some elements in science play a constitutive function, with the aim of overcoming some limitations of Friedman's (2001) account. More precisely, I focus on what I consider to be the gradualism implicit in Friedman's interpretation of the constitutive a priori, that is, the fact that it seems to allow for degrees of 'constitutivity'. I tease out such gradualism by showing that the constitutive character Friedman aims to track can (...) be captured by three features - namely, quasi-axiomaticity (QA), generative potential (GP), and empirical shielding (ES) - which are exhibited to a maximal degree by the examples Friedman deploys, particularly in his analysis of Newtonian mechanics. I argue that not all varieties of 'constitutivity' can be captured by the kind of gradualism implicit in Friedman's view, although developing the gradualism itself might provide useful insights. To show this, I analyse the function of the Hardy-Weinberg principle (HWP) in population genetics in terms of its QA, GP, and ES. Whereas the HWP does not count as constitutive in classical philosophical interpretations (Sober 1984), nor does it within Friedman's framework, it does nonetheless perform a minimally constitutive function. By means of historical details and considerations on the prospects of replacing the HWP, I show that the HWP is minimally constitutive by being a counterfactual instantiation of a paradigmatically constitutive stability principle, where the latter might itself be regarded as an enabling condition for a variety of modelling practices across the sciences. (shrink)

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

According to Joshua Alexander, philosophers use intuitions routinely as a form of evidence to test philosophical theories but experimental philosophy demonstrates that these intuitions are unreliable and unrepresentative.1 According to Herman Cappelen, philosophers never use intuitions as evidence (despite the vacuous sentential leader ‘intuitively’) and experimental philosophy lacks a rationale for its much-touted existence.2 That two books are diametrically opposed on methodology in philosophy is not noteworthy. But eyebrows might be raised at such contradictory accounts of the phenomenology of philosophical (...) inquiry. What is it that (analytic) philosophers do? Why is it so difficult to achieve consensus on the professional activities in which we engage? (shrink)

Using the context of controversies surrounding evolutionary developmental biology (EvoDevo) and the possibility of an Extended Evolutionary Synthesis, I provide an account of theory structure as idealized theory presentations that are always incomplete (partial) and shaped by their conceptual content (material rather than formal organization). These two characteristics are salient because the goals that organize and regulate scientific practice, including the activity of using a theory, are heterogeneous. This means that the same theory can be structured differently, in part because (...) theory presentations (as idealizations) intentionally depart from different features known to be present in a theory. Since there are diverse and potentially incompatible theory structures derived from heterogeneous goals found in scientific practices, a question arises about the absence of a unifying theory structure in the background. The notion of a “theory façade” offers a fruitful perspective on this potentially unsettling result. (shrink)

Günter Wagner’s Homology, Genes, and Evolutionary Innovation collects and synthesizes a vast array of empirical data, theoretical models, and conceptual analysis to set out a progressive research program with a central theoretical commitment: the genetic theory of homology. This research program diverges from standard approaches in evolutionary biology, provides sharpened contours to explanations of the origin of novelty, and expands the conceptual repertoire of evolutionary developmental biology. I concentrate on four aspects of the book in this essay review: the genetic (...) theory of homology and character identity networks; the implications for how we explain evolutionary novelties; the expanded set of concepts surrounding homology, and the epistemological conflicts between Wagner’s viewpoint and functionally-oriented evolutionary biology, as well as differences with other Evo–devo researchers. Together these have ramifications for how we interpret different explanatory approaches to evolutionary phenomena and understand relationships between the usefulness of concepts and the reality they represent. (shrink)

The many-faced relationship between chemistry and physics is one of the most discussed topics in the philosophy of chemistry. In his recent book Reducing Chemistry to Physics. Limits, Models, Consequences, Hinne Hettema conceives this relationship as a reduction link, and devotes his work to defend this position on the basis of a “naturalized” concept of reduction. In the present paper I critically review three kinds of issues stemming from Hettema’s argumentation: philosophical, scientific and methodological.

I propose a distinct type of robustness, which I suggest can support a confirmatory role in scientific reasoning, contrary to the usual philosophical claims. In model robustness, repeated production of the empirically successful model prediction or retrodiction against a background of independentlysupported and varying model constructions, within a group of models containing a shared causal factor, may suggest how confident we can be in the causal factor and predictions/retrodictions, especially once supported by a variety of evidence framework. I present climate (...) models of greenhouse gas global warming of the 20th Century as an example, and emphasize climate scientists’ discussions of robust models and causal aspects. The account is intended as applicable to a broad array of sciences that use complex modeling techniques. (shrink)