The comparative method grants epistemic access to the biological past. Comparing lineages provides empirical traction on both hypotheses about particular lineages and models of trait evolution. Understanding this evidential role is important. Although philosophers have recently turned their attention to relations of descent, little work exists exploring the status of evidence from convergences. I argue that, where they exist, convergences play a central role in the confirmation of adaptive hypotheses. I focus on ‘analogous inferences’, show how such inferences ought to (...) be analysed and suggest three methods for strengthening their evidential weight. 1 Introduction2 Analogous Inferences2.1 Adaptive explanations and analogies2.2 Analogous inferences2.3 Scope, grain, and specificity3 Parallel Modelling, Integrated Explanations, and Convergent Modelling3.1 Parallel modelling3.2 Integrated explanations3.1 Convergent modelling4 Conclusion. (shrink)

The growing range of methods for statistical model selection is inspiring new debates about how to handle the potential for conflicting results when different methods are applied to the same data. While many factors enter into choosing a model selection method, we focus on the implications of disagreements among scientists about whether, and in what sense, the true probability distribution is included in the candidate set of models. While this question can be addressed empirically, the data often provide inconclusive results (...) in practice. In such cases, we argue that differences in prior metaphysical views about the local adequacy of the models can produce underdetermination of results, even for the same data and candidate models. As a result, data alone are sometimes insufficient to settle rational beliefs about nature. (shrink)

The dominant view today on evolutionary progress is that it has been thoroughly debunked. Even value-neutral progress concepts are seen to lack important theoretical underpinnings: natural selection provides no rationale for progress, and natural selection need not even be invoked to explain large-scale evolutionary trends. In this paper I challenge this view by analysing how natural selection acts in heterogeneous environments. This not only undermines key debunking arguments, but also provides a selectionist rationale for a pattern of “evolutionary unfolding”, where (...) life radiates across an increased range of exploitation of environmental heterogeneity. (shrink)

The dominant theory of the evolution of moral cognition across a variety of fields is that moral cognition is a biological adaptation to foster social cooperation. This chapter argues, to the contrary, that moral cognition is likely an evolutionary exaptation: a form of cognition where neurobiological capacities selected for in our evolutionary history for a variety of different reasons—many unrelated to social cooperation—were put to a new, prosocial use after the fact through individual rationality, learning, and the development and transmission (...) of social norms. This chapter begins with a brief overview of the emerging behavioral neuroscience of moral cognition. It then outlines a novel theory of moral cognition that I have previously argued explains these findings better than alternatives. Finally, it shows how the evidence for this theory of moral cognition and human evolutionary history together suggest that moral cognition is likely not a biological adaptation. Instead, like reading sheet music or riding a bicycle, moral cognition is something that individuals learn to do—in this case, in response to sociocultural norms created in our ancestral history and passed down through the ages to enable cooperative living. (shrink)

Despite an enormous philosophical literature on models in science, surprisingly little has been written about data models and how they are constructed. In this paper, I examine the case of how paleodiversity data models are constructed from the fossil data. In particular, I show how paleontologists are using various model-based techniques to correct the data. Drawing on this research, I argue for the following related theses: first, the ‘purity’ of a data model is not a measure of its epistemic reliability. (...) Instead it is the fidelity of the data that matters. Second, the fidelity of a data model in capturing the signal of interest is a matter of degree. Third, the fidelity of a data model can be improved ‘vicariously’, such as through the use of post hoc model-based correction techniques. And, fourth, data models, like theoretical models, should be assessed as adequate for particular purposes. (shrink)

In a pioneering book, Philosophy of Microbiology, Maureen O’Malley argues for the philosophical importance of microbes through an examination of their impact on ecosystems, evolution, biological classification, collaborative behavior, and multicellular organisms. She identifies many understudied conceptual issues in the study of microbes. If philosophers follow her lead, the philosophy of biology will be expanded and enriched.

According to one large family of views, scientific explanations explain a phenomenon (such as an event or a regularity) by subsuming it under a general representation, model, prototype, or schema (see Bechtel, W., & Abrahamsen, A. (2005). Explanation: A mechanist alternative. Studies in History and Philosophy of Biological and Biomedical Sciences, 36(2), 421–441; Churchland, P. M. (1989). A neurocomputational perspective: The nature of mind and the structure of science. Cambridge: MIT Press; Darden (2006); Hempel, C. G. (1965). Aspects of scientific (...) explanation. In C. G. Hempel (Ed.), Aspects of scientific explanation (pp. 331–496). New York: Free Press; Kitcher (1989); Machamer, P., Darden, L., & Craver, C. F. (2000). Thinking about mechanisms. Philosophy of Science, 67(1), 1–25). My concern is with the minimal suggestion that an adequate philosophical theory of scientific explanation can limit its attention to the format or structure with which theories are represented. The representational subsumption view is a plausible hypothesis about the psychology of understanding. It is also a plausible claim about how scientists present their knowledge to the world. However, one cannot address the central questions for a philosophical theory of scientific explanation without turning one’s attention from the structure of representations to the basic commitments about the worldly structures that plausibly count as explanatory. A philosophical theory of scientific explanation should achieve two goals. The first is explanatory demarcation. It should show how explanation relates with other scientific achievements, such as control, description, measurement, prediction, and taxonomy. The second is explanatory normativity. It should say when putative explanations succeed and fail. One cannot achieve these goals without undertaking commitments about the kinds of ontic structures that plausibly count as explanatory. Representations convey explanatory information about a phenomenon when and only when they describe the ontic explanations for those phenomena. (shrink)

Historical scientists frequently face incomplete data, and lack direct experimental access to their targets. This has led some philosophers and scientists to be pessimistic about the epistemic potential of the historical sciences. And yet, historical science often produces plausible, sophisticated hypotheses. I explain this capacity to generate knowledge in the face of apparent evidential scarcity by examining recent work on Thylacoleo carnifex, the ‘marsupial lion’. Here, we see two important methodological features. First, historical scientists are methodological omnivores, that is, they (...) construct purpose-built epistemic tools tailored to generate evidence about highly specific targets. This allows them to produce multiple streams of independent evidence and thus maximize their epistemic reach. Second, investigative scaffolding: research proceeds in a piece-meal fashion, information only gaining evidential relevance once certain hypotheses are well supported. I illustrate scaffolding in a discussion of the nature of functional ascription in paleobiology. Frequently, different senses of ‘function’ are not discriminated during paleobiological investigation—something which can mar adaptationist investigations of extant organisms. However, I argue that, due to scaffolding, conflating senses of ‘function’ can be the right thing to do. Coarse-grained functional hypotheses are required before it is clear what evidence could discriminate between more fine-grained ones. I draw on omnivory and scaffolding to argue that pessimists make a bad empirical bet. It is a bad idea to bet against the epistemic fortunes of such opportunistic and resourceful scientists, especially when we have reason to think we will systematically underestimate the amount of evidence ultimately available to them. (shrink)

Caitlin Wylie’s “Preparing Dinosaurs: the work behind the scenes” (MIT Press 2021) provides a rich ethnographic analysis of the work of fossil preparators. On her account, knowledge in vertebrate paleontology is mediated through a three-way division of labour between paleontologists, preparators and volunteers, each with their own role, expertise and responsibility. In this review, I develop her notion of ‘preparation as knowledge’, focusing in particular on the nature of objectivity in paleontological knowledge and on the middle-road she indicates between constructivist (...) and realist approaches to epistemology. (shrink)

Is the cultural evolution of morality fairly contingent? Could cultural evolution have easily led humans to moral norms and judgments that are mostly false by our present lights? If so, does it matter philosophically? Yes, or so we argue. We empirically motivate the contingency of cultural evolution and show that it makes two major philosophical contributions. First, it shows that moral objectivists cannot explain the reliability of our moral judgments and thus strengthens moral debunking arguments. Second, it shows that the (...) reliability of our moral judgments is evidence for theism over metaphysical naturalism. (shrink)

“Ancient DNA Research” is the practice of extracting, sequencing, and analyzing degraded DNA from dead organisms that are hundreds to thousands of years old. Today, many researchers are interested in adapting state-of-the-art molecular biological techniques and high-throughput sequencing technologies to optimize the recovery of DNA from fossils, then use it for studying evolutionary history. However, the recovery of DNA from fossils has also fueled the idea of resurrecting extinct species, especially as its emergence corresponded with the book and movie Jurassic (...) Park in the 1990s. In this paper, I use historical material, interviews with scientists, and philosophical literature to argue that the search for DNA from fossils can be characterized as a data-driven and celebrity-driven practice. Philosophers have recently argued the need to seriously consider the role of data-driven inquiry in the sciences, and likewise, this history highlights the need to seriously consider the role of celebrity in shaping the kind of research that gets pursued, funded, and ultimately completed. On this point, this history highlights that the traditional philosophical and scientific distinctions between data-driven and hypothesis-driven research are not always useful for understanding the process and practice of science. Consequently, I argue that the celebrity status of a particular research practice can be considered as a “serious epistemic strategy” that researchers, as well as editors and funders, employ when making choices about their research and publication processes. This interplay between celebrity and methodology matters for the epistemology of science. (shrink)

A key issue in the philosophy of biology is evolutionary contingency, the degree to which evolutionary outcomes could have been different. Contingency is typically contrasted with evolutionary convergence, where different evolutionary pathways result in the same or similar outcomes. Convergences are given as evidence against the hypothesis that evolutionary outcomes are highly contingent. But the best available treatments of contingency do not, when read closely, produce the desired contrast with convergence. Rather, they produce a picture in which any degree of (...) contingency is compatible with any degree of convergence. This is because convergence is the repeated production of a given outcome from different starting points, and contingency has been defined without reference to the size of the space of possible outcomes. In small spaces of possibilities, the production of repeated outcomes is almost assured. This paper presents a definition of contingency which includes this modal dimension in a way that does not reduce it to the binary notion of contingency found in standard modal logic. The result is a conception of contingency which properly contrasts with convergence, given some domain of possibilities and a measure defined over it. We should therefore not ask whether evolution is contingent or convergent simpliciter, but rather about the degree to which it is contingent or convergent in various domains, as measured in various ways. (shrink)

Our epistemic access to the past is infamously patchy: historical information degrades and disappears and bygone eras are often beyond the reach of repeatable experiments. However, historical scientists have been remarkably successful at uncovering and explaining the past. I argue that part of this success is explained by the exploitation of dependencies between historical events, entities, and processes. For instance, if sauropod dinosaurs were hot blooded, they must have been gluttons; the high-energy demands of endothermy restrict sauropod grazing strategies. Understanding (...) such dependencies extends our reach into the past in spite of incomplete data. In addition, this serves as a counterexample to two accounts of method in the historical sciences. By one, historical science proceeds by identifying ‘smoking guns’: traces that discriminate between live hypotheses. By the other, historical hypotheses are supported by consilience: the convergence of independent lines of evidence. However, testing for ‘coherency’ between past hypotheses also plays a critical role in historical confirmation. Just as historical scientists exploit dependencies between past entities and present entities to infer what the past was like, they also exploit dependencies between past entities themselves. I do not suggest that archetypical historical science proceeds in this manner. Rather, the lesson I draw is that historical methodology cannot be characterized as archetypically relying on one method or another. Historical science is at base opportunistic, and is resistant to unitary analyses. 1 Introduction2 Snowballs and Explosions: The Basic Idea3 Were Sauropods Endothermic?4 Dependent Entities and Interdependent Explanations5 Smoking Guns and Consilience. (shrink)

This article defends a conception of philosophy popular outside the discipline but unpopular within it: that philosophy is unified by a concern with the meaning of life. First, it argues against exceptionalist theses according to which philosophy is unique among academic disciplines in not being united by a distinctive subject matter. It then presents a positive account, showing that the issue of the meaning of life is uniquely able to reveal unity between the practical and theoretical concerns of philosophy, while (...) meeting a range of desiderata for a typical specification of subject matter. After showing how recent analytic work on “the meaning of life” has conflated the traditional question with issues of social meaningfulness, it offers an explanation of why the traditional question has become marginalised in philosophy. The reasons are not good, however, so it concludes that philosophy should embrace its popular image. (shrink)

Can we be realists about a general category but pluralists about concepts relating to that category? I argue that paleobiological methods of delineating species are not affected by differing species concepts, and that this underwrites an argument that species concept pluralists should be species category realists. First, the criteria by which paleobiologists delineate species are ‘indifferent’ to the species category. That is, their method for identifying species applies equally to any species concept. To identify a new species, paleobiologists show that (...) interspecies processes, such as phenotypic plasticity, sexual dimorphism, or ontogenetic diversity, are a worse explanation of the variance between specimens than intraspecies processes. As opposed to operating under a single or plurality of species concepts, then, paleobiologists use abductive inferences, which would be required regardless of any particular species concept. Second, paleobiologists are frequently interested in large-scale, long-term morphological patterns in the fossil record, and resolving the fine-grained differences which result from different species concepts is irrelevant at those scales. I argue that this claim about paleobiological practice supports what I call ‘indifference realism’ about the species category. The indifference realist argues that when legitimate investigation is indifferent to a plurality of concepts, we should be realists about the category those concepts pertain to. (shrink)

George McGhee’s book “Convergent Evolution: limited forms most beautiful” provides an extensive survey of biological convergence. This paper has two main aims. First, it examines the theoretical claims McGhee makes about convergent evolution—specifically criticizing his use of a total morphospace to understand contingency and his assumption that functional constraints are non-contingent. Second, it sketches a group of important conceptual challenges facing researchers interested in convergence.

In a recent paper, Chris Haufe paints a provocative portrait of the late paleontologist Stephen Jay Gould. His principal aim is to resolve a “paradox” arising from a prima facie inconsistent pair of commitments: Gould believed that the biological facts could have been otherwise, and Gould believed that there are evolutionary laws. In order to resolve this paradox, Haufe makes two substantive claims: Gould was aware of the challenges that the Replay Thesis posed for a law-centered science of evolution, even (...) early in his career, and Gould endeavored to meet these challenges by deploying the “species-as-particles approach.” In this paper, I put pressure on both of these claims. By examining the goals and methods of Gould’s first “nomothetic research program,” the science of form, I show that it does not fit the picture of nomothetic science that Haufe illustrates. Additionally, I show that no straightforward connection exists between Gould’s understanding of contingency and his adoption of the species-as-particles approach. I propose that Gould’s career can be usefully split into three periods, each of which employed a distinct strategy for establishing distinctively paleontological contributions to evolutionary theory. (shrink)

This paper offers a paleobiological perspective on the debate concerning the possible use of biotechnology to bring back extinct species. One lesson from paleobiology is that extinction selectivity matters in addition to extinction rates and extinction magnitude. Combining some of Darwin’s insights about artificial selection with the theory of species selection that paleobiologists developed in the 1970s and 1980s provides a useful context for thinking about de-extinction. Using recent work on the prioritization of candidate species for de-extinction as a test (...) case, the paper argues that de-extinction would be a form of artificial species selection in which humans influence which species persist vs. go extinct. This points to a serious gap in our ethical theory: Much work has been done to clarify the value of biological diversity, but we also need theoretical guidance for decisions that amount to species sorting, and that will shape the macroevolutionary future. (shrink)

Lately there has been a wave of criticism of the concept of living fossils. First, recent research has challenged the status of paradigmatic living fossil taxa, such as coelacanths, cycads, and tuataras. Critics have also complained that the living fossil concept is vague and/or ambiguous, and that it is responsible for misconceptions about evolution. This paper defends a particular phylogenetic conception of living fossils, or taxa that exhibit deep prehistoric morphological stability; contain few extant species; and make a high contribution (...) to phylogenetic diversity. The paper shows how this conception of living fossils can make sense of recent research on contested cases. The phylogenetic living fossil concept has both theoretical and practical importance: theoretical, because it picks out an important explanatory target for evolutionary theory; and practical, because it picks out taxa that we might wish to prioritize for conservation. The best way to defend the concept of living fossils is to get clearer about the reasons for defending living fossil taxa. (shrink)

This paper examines Karl Alfred von Zittel’s practice in order to uncover the roots of so-called idiographic paleontology. The great American paleontologist Stephen Jay Gould (1941–2002) defined the discipline of idiographic paleontology as illustration and description of the morphological features of extinct species. However, this approach does not investigate macroevolutionary patterns and processes. On the contrary, the paleobiological revolution of the 1970s implemented an epistemic methodology that illustrates macrovelutionary patterns and laws by combining idiographic data with a nomothetic form of (...) explanation. This article elucidates the features of the idiographic data as well as the acquired knowledge coupled with this approach. First of all, Heinrich G. Bronn’s (1800–1862) statistical method is analyzed. Zittel’s practice arose as a reaction against the approximate conclusions reached by Bronn’s quantitative approach. Second, the details of Zittel’s methodology are described in order to bring out its peculiarities. The microscope played a pivotal role in creating and forming Zittel’s morphological data. This analysis sheds new light on the reasons behind the so-called ideographic paleontology, thus revising Gould’s historical reconstruction, as well as on the notion of paleontological data. However, even though Zittel aimed at reaching precise and stable conclusions, his data cannot be used for elucidating evolutionary mechanisms: they are scientific in a purely descriptive sense, but completely useless for biological investigations. Finally, this paper examines how Zittel’s methodology affects the contemporary paleobiological enterprise and thereby reflects upon the notion of natural history. (shrink)

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

The distinction between idiographic science, which aims to reconstruct sequences of particular events, and nomothetic science, which aims to discover laws and regularities, is crucial for understanding the paleobiological revolution of the 1970s and 1980s. Stephen Jay Gould at times seemed conflicted about whether to say (a) that idiographic science is fine as it is or (b) that paleontology would have more credibility if it were more nomothetic. Ironically, one of the lasting results of the paleobiological revolution was a new (...) way of doing historical science that defies categorization as idiographic or nomothetic. Yet the tension between (a) and (b) persists in some recent work in the philosophy of science, with Carol Cleland defending a version of (a) and Dan McShea and Robert Brandon defending a version of (b). In placing Cleland's work into conversation with that of McShea and Brandon, this paper defends a third (c) synthetic approach that emphasizes the blending of idiographic and nomothetic work. (shrink)

The objective of this dissertation is to write the first pages of the biography of paleobiological data. I will focus on i) the genesis of this kind of data as it emerged in German stratigraphy and paleontology between the mid 19th and the early 20th centuries and ii) how the conceptualization of the paleontological data was reformulated and taken as the starting point for studying the patterns of the diversity of life in deep time between the 1940s and 70s. This (...) is the turning point that marks the ‘coming into being’ of specifically paleobiological data. I will reconstruct in detail how it was possible to transform an incomplete and misleading material object — the fossil record that can be admired in a museum —into a no longer misleading source of knowledge. I will namely describe the genesis of the paleobiological practice by retracing the encounter of two different approaches to the fossil record between the mid 19th and early 20th centuries in German academia and their later diffusion into English-speaking countries. (shrink)