Philosophers of science sometimes seem to imply that there are evolutionary models in which a counterfactual infinite population of organisms plays a crucial role. As is sometimes noted, this idea is incoherent if “infinite population” is understood literally. This paper uses case studies of modeling in evolutionary biology to examine roles that “infinite population”, and assumptions about random drift, play in modeling practices. Sometimes various effects of the absence of drift are understood as having to do with limits as population (...) size goes toward infinity; in other cases these effects are conceptualized as having to do with large population sizes. Some models make assumptions about population size and effects of drift that might seem inconsistent: in some cases drift is included in part of a model, but excluded in another, or excluded even though population size is treated as finite. Because of such facts, I argue that there is no fixed set of assumptions associated with drift or its absence, and that there is no clear meaning for “infinite population” and similar terms. Rather “infinite population” is figurative language that is merely associated with various assumptions about the absence of drift. (shrink)

The idea that selection can go in opposite directions or, more generally, be independent at different levels is well entrenched in both the biological and philosophical literatures. However, this idea is difficult to render precise. On the face of it, it seems unclear how two levels of selection could conflict with one another – and thus be independent if they ultimately refer to the same Darwinian substrate. In this paper, I present an analysis of this problem. I argue that it (...) is impossible for selection at one level to be independent from selection at a different level if independence is to be understood in a strong (metaphysical) sense. However, I propose that independence can be understood in a weaker sense, so long as our conception of independence does not violate the metaphysical dependence of the higher levels on the lower ones. From there, I argue that none of the notions of particle-level or collective-level selection used in the classical formal approaches to multilevel selection capture this weaker form of independence. Finally, I propose a different approach that is compatible with both metaphysical dependence and the weaker form of independence outlined in this paper. (shrink)

The role of reciprocal causation in Extended Evolutionary Synthesis (EES) is controversial. Proponents of EES argue that reciprocal causation is a key innovation, underpinning the necessity of EES. Conversely, critics of the EES maintain that Standard Evolutionary Theory (SET) adequately encompasses the concept of reciprocal causation, challenging the need for EES. This skepticism is rooted in two primary critiques. First, the mischaracterization of causal dynamics within SET by EES advocates leads to a misrepresentation of SET. Second, the oversight of how (...) SET incorporates and acknowledges instances of reciprocal causation leads to claims about the empirical inaptness of SET. As a result, the debate has reached an impasse, with limited progress towards a constructive examination of reciprocal causation’s significance to evolutionary explanations. This paper introduces the scope argument, which examines reciprocal causation through timescales and grain of explanations. This approach revitalizes the debate in two ways. First, reframing the debate in terms of scope clarifies the role of reciprocal causation by allowing research programs to specify targets of explanation. Second, the elements of scope (timescales and grain) elucidate the epistemic advantage of reciprocal causation in the respective research programs in question. (shrink)

The cell’s ability to metabolize foodstuffs, synthesize proteins and nucleic acids, and transduce extracellular signals, all rely on an intricate intracellular network of biological systems. These biosystems are the dynamic manifestations of the molecular pathways that define them and arise when these molecular pathways are activated. In this paper, I ask if the transformation from pathway to biosystem (abbr., bioSip, for intracellular pathway biosystem) is accompanied by a change in ontological status, and if so, what this new status is. After (...) introducing key biochemical concepts, including the difference between pathway and biosystem, and the concept of enzyme coupling that transforms an ensemble of enzymes into a bioSip, I analyze the ontological status of bioSips, specifically asking if the empirical data support the view that bioSips exist in nature as ontological unities, as actualities. I conclude that certain highly structured bioSips, known as metabolons, are indeed actualities. Finally, I explore the metaphysical foundations for the ontological unity of metabolons, considering three metaphysical systems that emphasize the dynamic and relational nature of reality: process philosophy, Aristotelian-Scholastic substance philosophy, and Ivor Leclerc’s philosophy of nature. (shrink)

Paleobiology is not only a science of the deep past: it is a science of deep possibility. Drawing on recent speculative reconstructions of Spinosaurus aegyptiacus, I sketch a new account of paleobiological reconstruction. Fossils, as opposed to testing causal hypotheses, are used to characterise and evidence the ‘central subjects’ of paleobiological reconstruction, in this instance, particular dinosaur taxa. These central subjects are then situated in various ‘profiles’, representational tools which isolate particular traits across several dimensions in order to apply comparative (...) methods which generate and test often modal hypotheses. I suggest this represents a particular phenomena-driven mode of exploring possibility, one with distinct advantages over approaches more common in theoretical evolutionary biology. (shrink)

Studies of the history of life provide an interesting case study of how the questions scientists can ask, and from which they expect reliable answers, change over time. Some of these changes reflect the introduction of new technology or methodological advances in other fields that open new opportunities; other changes reflect an evolving perspective on what constitutes important research questions or the integration of multiple streams of information. In this contribution, I consider the changing nature of questions in paleontology, largely (...) focusing on English-speaking paleontologists since the mid-twentieth century. Rather than bemoaning the field’s limitations, paleontologists have pioneered techniques to identify and often correct preservation and collecting biases in the fossil record. Rigorous methods to infer and test phylogenies have been integrated with molecular clock studies to infer branch-points in phylogeny, and with insights from comparative developmental studies, which together inform our understanding of evolutionary dynamics, particularly novelty. Together, these advances have changed the questions paleontologists can address about the history of life, eliminating some questions (particularly in paleoecology), but greatly expanding research programs in other areas as well as collaborations with biologists and other Earth scientists. I suggest that the questions driving paleontologists have evolved from primarily descriptive and explanatory to increasingly analytical and integrative. These trends are briefly illustrated with examples from studies of the Ediacaran-Cambrian diversification of animals, and from studies of mass extinctions. (shrink)

Existing accounts of data are unclear about whether the epistemic role objects play makes them data, or whether data have to be produced by human interaction with the world – these two features can come apart. I illustrate this ambiguity using the case of fossil data, which have rich histories and undergo many processes before they are encountered by humans. I then outline several philosophical positions that would resolve the ambiguity moving forward, and elaborate on my preferred option.

The processes of producing scientific knowledge rely on the temporality of data, yet they also obscure this relationship. Scientists hope that knowledge claims can stand relatively independent from their context of production. Instead, a more realistic and trustworthy view would be to embrace data’s history and “journey” (Leonelli and Tempini 2020) as a component of the knowledge claims that these data inspire. These journeys describe how data and people interact and thereby influence each other’s identity and epistemic worth. In this (...) paper, I propose a model to help philosophers and other analysts pay closer attention to the people who work with scientific data, specifically by considering how these practitioners conceptualize time. I argue that how practitioners experience time reflects the personal, professional, epistemic, and ethical values that guide their decisions about how to do science. These conceptions of time differ by profession, career stage, identity, institutional context, and other factors specific to practitioners’ lives as well as their scientific or disciplinary culture. I draw from two case studies of vertebrate fossils to illustrate how various conceptions of time co-exist for practitioners, as indicators of the values that guide practitioners’ decisions as they do scientific work. (shrink)

A significant and longstanding debate in philosophy of biology has centered around biological individuality. Although there have been numerous attempts to articulate a plausible and unifying view of what makes something a biological individual, the results are often conflicting and non-coextensive. In spite of these disputes, an open consensus around a few general ideas has surfaced (Pradeu 2016a). One common assumption that has been carried over with the consensus is that biological individuality is an intrinsic property of biological entities (Clarke (...) 2016a). This tendency is reflected in the properties typically selected as criteria: what makes something an individual is quite often a property that biological entities themselves possess. I draw on Ellen Clarke’s (2013) evolutionary account of biological individuality, research about the evolution and maintenance of cooperation in the origins of multicellularity (Brockhurst et al. 2007; Gulli et al. 2019), and important parts of the consensus around biological individuality to argue against this trend. What makes something a biological individual is not always something about the entities in question. I show that there are environmental mechanisms capable of acting as individuation mechanisms in circumstances that resemble early transition stages, or in situations where individuality departs from paradigm cases. Therefore, biological individuality is not necessarily an intrinsic property. (shrink)

Relative frequency controversies, so common in the biological sciences, pose something of a puzzle. Why do biologists routinely engage in disputes that (a) are rarely settled and (b) arguably wouldn’t yield interesting knowledge even if they were? Recent work suggests that relative frequency controversies can lead biologists to increase their understanding of the modal profile of the processes under dispute. Here, we consider some further consequences of this view. We contend that relative frequency controversies can generate recurrent, transient underdetermination about (...) which causes are responsible for producing particular effects. As a result, the increases in understanding these controversies provide can come with decreases in biologists’ ability to offer warranted explanations. We argue that this fits with a toolkit view of biological theory, and suggest some implications for the scientific realism debate as it pertains to biological science. (shrink)

In this manifesto for a more comprehensive account of evolution by natural selection (ENS), we draw on Hull’s framework to expand the reach of Darwinian explanations. His approach is centered on the notions of interactor and replicator. He (and many others following him) defines the interactor in terms of cohesiveness. Often, such cohesiveness is cashed out by the vertical transmission to the next generation of the replicators that constitute the interactors. While we maintain the importance of the reciprocal influence of (...) interactors and replicators (the differential extinction and proliferation of interactors leads to the differential extinction and proliferation of the replicators that produce them) central to Hull’s framework, we downplay the importance of the cohesiveness of interactors and eliminate any need for lineage formation among them. This suggested revision of the interactor synthesizes various recent contributions in the field, and it allows the interactor/replicator framework to tackle more complex entities. Our approach, however, stands in stark opposition to the classical approach to ENS centered on lineage formation. In this paper, we present our view and argue that it should replace the classical approach in structuring future work in evolutionary biology. (shrink)

This paper addresses a relatively new mode of ecological research: data synthesis studies. Data synthesis studies involve reusing data to create a general model as well as a reusable, aggregated dataset. Using a case from movement ecology, I analyse the trade-offs and strategies involved in data synthesis. Like theoretical ecological modelling, I find that synthesis studies involve a modelling trade-off between generality, precision and realism; they deal with this trade-off by adopting a pragmatic kludging strategy. I also identify an additional (...) trade-off, the synthesis trade-off, between making data easy to synthesise for a particular project, on the one hand, and facilitating data reuse for other projects, on the other. In response to this synthesis trade-off, researchers create flexible datasets that are relatively easy to use for particular projects and can be adjusted to suit some other purposes. The flexibility compromise is also found in broader open data efforts, making it a significant element in the future of data-intensive ecology. (shrink)