In an influential paper, Wendy Parker argues that agreement across climate models isn’t a reliable marker of confirmation in the context of cutting-edge climate science. In this paper, I argue that while Parker’s conclusion is generally correct, there is an important class of exceptions. Broadly speaking, agreement is not a reliable marker of confirmation when the hypotheses under consideration are mutually consistent—when, e.g., we’re concerned with overlapping ranges. Since many cutting-edge questions in climate modeling require making distinctions between mutually consistent (...) hypotheses, agreement across models will be generally unreliable in this domain. In cases where we are only concerned with mutually exclusive hypotheses, by contrast, agreement across climate models is plausibly a reliable marker of confirmation. (shrink)

I examine error diagnosis (model-model disagreement) in climate model intercomparisons including its difficulties, fruitful examples, and prospects for streamlining error diagnosis. I suggest that features of climate model intercomparisons pose a more significant challenge for error diagnosis than do features of individual model construction and complexity. Such features of intercomparisons include, e.g., the number of models involved, how models from different institutions interrelate, and what scientists know about each model. By considering numerous examples in the climate modeling literature, I distill (...) general strategies (e.g., employing physical reasoning and using dimension reduction techniques) used to diagnose model error. Based on these examples, I argue that an error repertoire could be beneficial for improving error diagnosis in climate modeling, although constructing one faces several difficulties. Finally, I suggest that the practice of error diagnosis demonstrates that scientists have a tacit-yet-working understanding of their models which has been under-appreciated by some philosophers. (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)

A general view in philosophy of science says that the appropriateness of an object to act as a surrogate depends on the user’s decision to utilize it as such. This paper challenges this claim by examining the role of surrogative reasoning in high-throughput sequencing technologies as they are used in contemporary microbiome science. Drawing on this, we argue that, in technology-driven surrogates, knowledge about the type of inference practically permitted and epistemically justified by the surrogate constrains their use and thus (...) puts a limit to the user’s intentions to use any object as a surrogate for what they please. Ignoring this leads to a serious epistemic misalignment, which ultimately prevents surrogative reasoning. Thus, we conclude that knowledge about the type of surrogate reasoning that the technologies being used allow is fundamental to avoid misinterpreting the consequences of the data obtained with them, the hypothesis this data supports, and what these technologies are surrogates of. (shrink)

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

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)

The units or levels of selection debate concerns the question of what kind of biological systems are stable enough that part of their evolution is a result of the process of natural selection acting at their level. Traditionally, the debate has concerned at least two different, though related, questions: the question of the level at which interaction with the environment occurs, and the question of the level at which reproduction occurs. In recent years, biologists and philosophers have discussed a new (...) aspect of this debate, namely the possibility that certain multi-species consortia formed by a host and its microbiome may act as a unit of selection. This thesis, however, has not been without criticism, as it is doubtful that such consortia could meet the conditions required to achieve the degree of stability that would allow them to experience natural selection. The purpose of this paper is to systematically examine such criticisms and to defend the thesis that the holobiont/hologenome can act as a genuine level of selection both in the form of an interactor and in the form of a reproducer. To do so, it will be argued that the microbiome should be characterized in functional rather than taxonomic terms. (shrink)

According to simulationism, the function of episodic memory is not to remember the past, but to help construct representations of possible future episodes, by drawing together features from different experiential sources. This article suggests that the relationship between the traditional storehouse view, on which the function of memory is remembering, and the simulationist approach is more complicated than has been typically acknowledged. This is attributed, in part, to incorrect interpretations of what remembering on the storehouse view requires. Further, by appeal (...) to function pluralism, the article questions both the assumption that the traditional view and simulationism are inconsistent, and the simulationist’s inference to the best explanation strategy that is based upon this assumption. The article then provides an evaluation of the simulationist argument against the traditional view, and finds it in need of further support. (shrink)

We address the controversy in the literature concerning the definition of holobionts and the apparent constraints on their evolution using concepts from community population genetics. The genetics of holobionts, consisting of a host and diverse microbial symbionts, has been neglected in many discussions of the topic, and, where it has been discussed, a gene-centric, species-centric view, based in genomic conflict, has been predominant. Because coevolution takes place between traits or genes in two or more species and not, strictly speaking, between (...) species, it may affect some traits but not others in either host or symbiont. Moreover, when interacting species pairs are embedded in a larger community, indirect ecological effects can alter the expected pairwise dynamics. Mode of symbiont transmission and the degree of host inbreeding both affect the extent of microbial mixing across host lineages and thereby the degree to which selection on one trait of either partner affects other aspects of a holobiont phenotype. We discuss several potential defining criteria for holobionts using community genetics and population genetics models, suggesting their application and limitations. Using community genetics models, we show how conflict between genomes can be self-limiting, while cooperation and mutualism tend to be self-accelerating. It is likely that this bias in the evolutionary dynamics of interaction between hosts and symbionts is an important feature of holobionts. This bias in the evolutionary dynamic could contribute to explaining the absence of cheaters from natural mutualisms, although cheaters are predicted by gene-centered conflict theory to cause the evolutionary instability of mutualisms. Additionally, it may help explain the more frequent origin of mutualisms from parasitic than from free-living systems, an evolutionary trajectory opposite to that predicted by genome conflict theory. (shrink)

This paper aims to provide a philosophical and theoretical account of biological communication grounded in the notion of organisation. The organisational approach characterises living systems as organised in such a way that they are capable to self-produce and self-maintain while in constant interaction with the environment. To apply this theoretical framework to the study of biological communication, we focus on a specific approach, based on the notion of influence, according to which communication takes place when a signal emitted by a (...) sender triggers a change in the behaviour of the receiver that is functional for the sender itself. We critically analyse the current formulations of this account, that interpret what is functional for the sender in terms of evolutionary adaptations. Specifically, the adoption of this etiological functional framework may lead to the exclusion of several phenomena usually studied as instances of communication, and possibly even of entire fields of investigation such as synthetic biology. As an alternative, we reframe the influence approach in organisational terms, characterising functions in terms of contributions to the current organisation of a biological system. We develop a theoretical account of biological communication in which communicative functions are distinguished from other types of biological functions described by the organisational account (e.g. metabolic, ecological, etc.). The resulting organisational-influence approach allows to carry out causal analyses of current instances of phenomena of communication, without the need to provide etiological explanations. In such a way it makes it possible to understand in terms of communication those phenomena which realise interactive patterns typical of signalling interactions – and are usually studied as such in scientific practice – despite not being the result of evolutionary adaptations. Moreover, this approach provides operational tools to design and study communicative interactions in experimental fields such as synthetic biology. (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)

Is there anything that members of each binary category of gender have in common? Even many non-essentialists find the lack of unity within a gender worrying as it undermines the basis for a common political agenda for women. One promising proposal for achieving unity is by means of a shared historical lineage of cultural reproduction with past binary models of gender. I demonstrate how such an account is likely to take on board different binary and also non-binary systems of gender. (...) This implies that all individuals construed as members of the category, “women” are in fact not members of the same historical kind after all! I then consider different possible means of modifying the account but conclude negatively: the problem runs deeper than has been appreciated thus far. (shrink)

Some methodological adaptationists hijacked the term “exaptation,” and took an occasion of Stephen Jay Gould’s misspeaking as confirmation that it possessed an evolutionarily “designed” function and was a version of an adaptation, something it was decidedly not. Others provided a standard of evidence for exaptation that was inappropriate, and based on an adaptationist worldview. This article is intended to serve as both an analysis of and correction to those situations. Gould and Elisabeth Vrba’s terms, “exaptation” and “aptation,” as originally introduced, (...) are very useful, unlike the faded adaptationist echo of “exaptation” devised by the methodological adaptationists, which has made the term incoherent. We will discuss how exaptation relates to function, to aptation, and to adaptation, both primary and secondary. These ideas have been rendered practically useless through their mistaken definitions and misapplications by evolutionary psychologists. (shrink)

Behavioural flexibility is often treated as the gold standard of evidence for more sophisticated or complex forms of animal cognition, such as planning, metacognition and mindreading. However, the evidential link between behavioural flexibility and complex cognition has not been explicitly or systematically defended. Such a defence is particularly pressing because observed flexible behaviours can frequently be explained by putatively simpler cognitive mechanisms. This leaves complex cognition hypotheses open to ‘deflationary’ challenges that are accorded greater evidential weight precisely because they offer (...) putatively simpler explanations of equal explanatory power. This paper challenges the blanket preference for simpler explanations, and shows that once this preference is dispensed with, and the full spectrum of evidence—including evolutionary, ecological and phylogenetic data—is accorded its proper weight, an argument in support of the prevailing assumption that behavioural flexibility can serve as evidence for complex cognitive mechanisms may begin to take shape. An adaptive model of cognitive-behavioural evolution is proposed, according to which the existence of convergent trait–environment clusters in phylogenetically disparate lineages may serve as evidence for the same trait–environment clusters in other lineages. This, in turn, could permit inferences of cognitive complexity in cases of experimental underdetermination, thereby placing the common view that behavioural flexibility can serve as evidence for complex cognition on firmer grounds. (shrink)

Lloyd analyzes every proposed evolutionary explanation of female orgasm and argues that all but one suffers from serious evidential errors. Lloyd attributes these errors to two main biases: androcentrism and adaptationism. This paper begins by arguing that the explanation Lloyd favors—the by-product account—is guilty of the androcentrism which supposedly implicates the other explanations of female orgasm with numerous evidential discrepancies. This suggests that there is another error afflicting orgasm research in addition to the biases Lloyd identities. I attempt to diagnose (...) and characterize this additional error. In short, I think the error is using an imprecise definition of the trait in question. Further, Lloyd takes her analysis to support Longino’s contextual empiricist model of scientific objectivity. I consider what implications this analysis has for contextual empiricism. Finally, I argue that theorizing about female orgasm should be done from a conceptual engineering approach. (shrink)

In evolutionary medicine, researchers characterize some outcomes as evolutionary mismatch. Mismatch problems arise as the result of organisms living in environments to which they are poorly adapted, typically as the result of some rapid environmental change. Depression, anxiety, obesity, myopia, insomnia, breast cancer, dental problems, and numerous other negative health outcomes have all been characterized as mismatch problems. The exact nature of evolutionary mismatch itself is unclear, however. This leads to a lack of clarity about the sorts of problems that (...) evolutionary mismatch can actually explain. Resolving this challenge is important not only for the evolutionary health literature, but also because the notion of evolutionary mismatch involves central concepts in evolutionary biology: fitness, evolution in changing environments, and so forth. In this paper, I examine two characterizations of mismatch currently in the literature. I propose that we conceptualize mismatch as a relation between an optimal environment and an actual environment. Given an organism and its particular physiology, the optimal environment is the environment in which the organism’s fitness is maximized: in other words, the optimal environment is that in which the organism’s fitness is as high as it can possibly be. The actual environment is the environment in which the organism actually finds itself. To the extent that there is a discordance between the organism’s actual and optimal environments, there is an evolutionary mismatch. In the paper, I show that this account of mismatch gives us the right result when other accounts fail, and provides useful targets for investigation. (shrink)

In the 20th century, genetic explanatory approaches became dominant in both developmental and evolutionary biological research. By contrast, physical approaches, which appeal to properties such as mechanical forces, were largely relegated to the margins, despite important advances in modeling. Recently, there have been renewed attempts to find balanced viewpoints that integrate both biological physics and molecular genetics into explanations of developmental and evolutionary phenomena. Here we introduce the 2017 SICB symposium “Physical and Genetic Mechanisms for Evolutionary Novelty” that was dedicated (...) to exploring empirical cases where both biological physics and developmental genetic considerations are crucial. To further contextualize these case studies, we offer two theoretical frameworks for integrating genetic and physical explanations: combining complementary perspectives and comprehensive unification. We conclude by arguing that intentional reflection on conceptual questions about investigation, explanation, and integration is critical to achieving significant empirical and theoretical advances in our understanding of how novel forms originate across the tree of life. (shrink)

The theory of evolution by natural selection is, perhaps, the crowning intellectual achievement of the biological sciences. There is, however, considerable debate about which entity or entities are selected and what it is that fits them for that role. This article aims to clarify what is at issue in these debates by identifying four distinct, though often confused, concerns and then identifying how the debates on what constitute the units of selection depend to a significant degree on which of these (...) four questions a thinker regards as central. (shrink)

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

Kevin Laland and colleagues have put forward a number of arguments motivating an extended evolutionary synthesis. Here I examine Laland et al.'s central concept of reciprocal causation. Reciprocal causation features in many arguments supporting an expanded evolutionary framework, yet few of these arguments are clearly delineated. Here I clarify the concept and make explicit three arguments in which it features. I identify where skeptics can—and are—pushing back against these arguments, and highlight what I see as the empirical, explanatory, and methodological (...) issues at stake. (shrink)

The current evolutionary taxonomy is biased towards traits that enhance the organism’s fitness. Here, an extended taxonomy aimed to correct this bias is proposed, which distinguishes among different categories of non-fitness traits based on their usefulness for the organism as well as their origin. It is suggested these new non-fitness categories could help to solve the controversy surrounding the term exaptation in evolutionary psychology.

In a scenario characterized by unpredictable developments, such as the recent COVID-19 pandemic, epidemiological models have played a leading part, having been especially widely deployed for forecasting purposes. In this paper, two real-world examples of modeling are examined in support of the proposition that science can convey inconsistent as well as genuinely perspectival representations of the world. Reciprocally inconsistent outcomes are grounded on incompatible assumptions, whereas perspectival outcomes are grounded on compatible assumptions and illuminate different aspects of the same object (...) of interest. In both cases, models should be viewed as expressions of specific assumptions and unconstrained choices on the part of those designing them. The coexistence of a variety of models reflects a primary feature of science, namely its pluralism. It is herein proposed that recent over-exposure to science’s inner workings and disputes such as those pertaining to models, may have led the public to perceive pluralism as a flaw—or more specifically, as disunity or fragmentation, which in turn may have been interpreted as a sign of unreliability. In conclusion, given the inescapability of pluralism, suggestions are offered as to how to counteract distorted perceptions of science, and thereby enhance scientific literacy. (shrink)

Feminist philosophers have discussed the prospects for assessing values empirically, particularly given the ongoing threat of sexism and other oppressive values influencing science and society. Some advocates of such tests now champion a “values as evidence” approach, and they criticize Helen Longino’s contextual empiricism for not holding values to the same level of empirical scrutiny as other claims. In this paper, we defend contextual empiricism by arguing that many of these criticisms are based on mischaracterizations of Longino’s position, overstatements of (...) certain claims, and false dichotomies. Her contextual empiricism not only allows for the empirical support and disconfirmation of values, but Longino explicitly discusses when values can be empirically adjudicated and emphasizes the crucial role of the community for standards of evidence. We support contextual empiricism and elaborate a less direct account of “values as heuristics” by reviewing Longino’s theory of evidence and then using a case study from Elisabeth Lloyd on the biology of female orgasm, demonstrating the disconfirmation of androcentric values in evolutionary science. Within Longino’s and Lloyd’s contextual empiricism, values do not get treated as empirical evidence to be directly assessed by individuals, but rather values are heuristic tools to build models whose use can be validated or invalidated by communities based on their empirical fruitfulness in the logic and pragmatics of research questions in specific historical and cultural contexts. (shrink)

In this paper we consider some questions surrounding whether or not regional climate models “add value,” a controversial issue in climate science today. We highlight some objections frequently made about regional climate models both within and outside the community of modelers, including several claims that regional climate models do not “add value.” We show that there are a number of issues involved in the latter claims, the primary ones centering on the fact that different research questions are being pursued by (...) the modelers making the complaints against regional climate models. Further issues focus on historical deficiencies of particular—but not generalizable—failures of individual regional models. We provide tools to sort out these different research questions and particular failures, and to improve communication and understanding surrounding added value in climate modeling and philosophy of climate science. (shrink)

What are the relevant values to the appraisal of research programs? This question remains hotly debated, as philosophers have recently proposed many lists of values potentially relevant to scientific appraisal. Surprisingly, despite being mentioned in many lists, little attention has been paid to fruitfulness. It is unclear how fruitfulness should be explicated, and whether it has any substantial role in scientific appraisal. In this paper, I argue we should explicate fruitfulness as the capacity to develop of research programs. Moreover, I (...) provide a novel strategy to assess and compare the fruitfulness of programs focused on their research questions and heuristics. To illustrate how this strategy would work, I will discuss a case study, namely the adaptationist program in evolutionary psychology. (shrink)

In multicellular organisms, cells are frequently programmed to die. This makes good sense: cells that fail to, or are no longer playing important roles are eliminated. From the cell’s perspective, this also makes sense, since somatic cells in multicellular organisms require the cooperation of clonal relatives. In unicellular organisms, however, programmed cell death poses a difficult and unresolved evolutionary problem. The empirical evidence for PCD in diverse microbial taxa has spurred debates about what precisely PCD means in the case of (...) unicellular organisms. In this article, we survey the concepts of PCD in the literature and the selective pressures associated with its evolution. We show that definitions of PCD have been almost entirely mechanistic and fail to separate questions concerning what PCD fundamentally is from questions about the kinds of mechanisms that realize PCD. We conclude that an evolutionary definition is best able to distinguish PCD from closely related phenomena. Specifically, we define “true” PCD as an adaptation for death triggered by abiotic or biotic environmental stresses. True PCD is thus not only an evolutionary product but must also have been a target of selection. Apparent PCD resulting from pleiotropy, genetic drift, or trade-offs is not true PCD. We call this “ersatz PCD.”. (shrink)

In this essay, I examine the usage of the term “just-so story.” I attempt to show that just-so storytelling can be seen as an epistemic concept that, in various ways, tackles the epistemological an...

In The Enigma of Reason, Mercier and Sperber (M&S) present and defend their interactionist account of reason. In this piece, I discuss briefly the points of agreement between M&S and myself and, more extensively, the points of disagreement, most of which pertain to details of the evolutionary components of their account. I discuss in particular the purported modular nature of reason; their account of myside bias as an optimum/adaptation; and the claim that reason thus construed must be an individual‐level and (...) not a group‐level adaptation. In the final section, I offer brief considerations on an alternative account of reasoning, where the focus is on how sociocultural environments may tune the social production and evaluation of arguments. (shrink)

After biologist Deborah Gordon made a series of experimental discoveries in the 1980s, she argued that a change in terminology regarding the division of labor among castes of specialists was needed. Gordon’s investigations of the interactive effects of ants in colonies led her to believe that the established approach Edward O. Wilson had pioneered was biased in a way that made some alternative candidate adaptive explanations invisible. Gordon argued that this was because the term “division of labor” implied a division (...) among specialists that was unwarranted, and proposed “task allocation” as a better description that did not bias research against the alternative causes she had discovered. Gordon’s empirical findings and theoretical proposals also vindicate the initial critics of Wilson’s human sociobiology who have been dismissed as political radicals, but her proposals have been widely misunderstood by many contemporary behavioral ecologists. The terminological and methodological confusions rampant in contemporary discourse can be clarified by applying a framework developed by Elisabeth Lloyd involving an analysis of the constraints imposed by different research questions. Applying this framework will show how the methodological problems involving description raised by the initial critics of Wilson’s human sociobiology extended to his analysis of ants, indicating that they were not challenging Wilson’s naturalistic approach to the study of human evolution, but rather his methods. It will also show how confusion over how Gordon’s proposed research questions have been conflated with the possible answers she has argued ought to be investigated. This in turn will clarify contemporary disputes over her proposal to abandon the term “division of labor.”. (shrink)