We characterize a type of functional explanation that addresses why a homologous trait originating deep in the evolutionary history of a group remains widespread and largely unchanged across the group’s lineages. We argue that biologists regularly provide this type of explanation when they attribute conserved functions to phenotypic and genetic traits. The concept of conserved function applies broadly to many biological domains, and we illustrate its importance using examples of molecular sequence alignments at the intersection of evolution and cell biology. (...) We use these examples to show how the study of conserved functions can integrate knowledge of a trait’s causal effects on fitness and its history of natural selection without invoking adaptation. We also show how conserved function provides a novel basis for addressing objections against evolutionary functions raised by Robert Cummins. (shrink)

A research community must share assumptions, such as about accepted knowledge, appropriate research practices, and good evidence. However, community members also hold some divergent assumptions, which they—and we, as analysts of science—tend to overlook. Communities with different assumed values, knowledge, and goals must negotiate to achieve compromises that make their conflicting goals complementary. This negotiation guards against the extremes of each group’s desired outcomes, which, if achieved, would make other groups’ goals impossible. I argue that this diversity, as a form (...) of value pluralism, regularly influences scientific practice and can make scientific evidence and knowledge more useful and more reliable. As an example, I examine vertebrate paleontology laboratories, which house a variety of workers with different training and priorities, particularly about the meaning of time. Specifically, scientists want to study fully prepared fossils immediately, conservators want to preserve fossils for future use, and preparators mediate between the other groups’ conflicting goals. After all, one cannot study a fossil encased in rock, and one cannot remove that rock without removing information from that specimen. In response, these coworkers articulate their assumptions in everyday deliberations about how scientific evidence should be made and used. I argue that this exchange of assumptions is crucial for a research community to achieve mutually beneficial compromises that benefit current and future knowledge construction. (shrink)

Philosophers of science are well aware that theories are underdetermined by data. But what about the data? Scientific data are selected and processed representations or pieces of nature. What is useless context and what is valuable specimen, as well as how specimens are processed for study, are not obvious or predetermined givens. Instead, they are decisions made by scientists and other research workers, such as technicians, that produce different outcomes for the data. Vertebrate fossils provide a revealing case of this (...) data-processing, because they are embedded in rock that often matches the fossils’ color and texture, requiring an expert eye to judge where the fossil/context interface is. Fossil preparators then permanently define this interface by chiseling away the material they identify as rock. As a result, fossil specimens can emerge in multiple possible forms depending on the preparator’s judgment, skill, and chosen tools. A prepared fossil then is not yet data but potential data, following Leonelli’s relational framework in which data are defined as evidence that scientists have used to support a proposed theory. This paper draws on ethnographic evidence to assess how scientists overcome this underdetermination of specimens, as potential data, in addition to the underdetermination of theories and of data, to successfully construct specimen-based knowledge. Among other strategies, paleontology maintains a division of labor between data-makers and theory-makers. This distinction serves to justify the omission of preparators’ nonstandard, individualized techniques from scientific publications. This separation has benefits for both scientists and technicians; however, it restricts knowledge production by preventing scientists from understanding how the pieces of nature they study were processed into researchable specimens. (shrink)

In this paper we argue that the difference between standard measurement and proxy measurement in paleoclimatology should not be understood in terms of ‘directness’. Measurements taken by climatologists to be paradigmatically non-proxy exhibit the kinds of indirectness that are thought to separate them proxy measurement. Rather, proxy measurements and standard measurements differ in how they account for confounding causal factors. Measurements are ‘proxy’ to the extent that the measurements require vicarious controls, while measurements are not proxy, but rather ‘standard’, to (...) the extent that the measurement apparatus provides sufficient physical control on its own. Guided by this account of proxy measurement, we then consider some of the challenges specific to historical proxy measurement and how it is that historical scientists address these challenges. Historical scientists rely on significant causal dependencies and naturally preserved signals to mitigate the influence of destructive processes over time. (shrink)

Several scholars observed that narratives about the human past are evaluated comparatively. Few attempts have been made, however, to explore how such evaluations are actually done. Here I look at a lengthy “contest” among several historiographic narratives, all constructed to make sense of another one—the biblical story of the conquest of Canaan. I conclude that the preference of such narratives can be construed as a rational choice. In particular, an easily comprehensible and emotionally evocative narrative will give way to a (...) complex and mundane one, when the latter provides a more coherent account of the consensually accepted body of evidence. This points to a fundamental difference between historiographic narratives and fiction, contrary to some influential opinions in the philosophy of historiography. Such historiographic narratives have similarities with hypotheses and narrative explanations in natural science. (shrink)

This article examines the effect of material evidence upon historiographic hypotheses. Through a series of successive Bayesian conditionalizations, I analyze the extended competition among several hypotheses that offered different accounts of the transition between the Bronze Age and the Iron Age in Palestine and in particular to the “emergence of Israel”. The model reconstructs, with low sensitivity to initial assumptions, the actual outcomes including a complete alteration of the scientific consensus. Several known issues of Bayesian confirmation, including the problem of (...) old evidence, the introduction and confirmation of novel theories and the sensitivity of convergence to uncertain and disputed evidence are discussed in relation to the model’s result and the actual historical process. The most important result is that convergence of probabilities and of scientific opinion is indeed possible when advocates of rival hypotheses hold similar judgment about the factual content of evidence, even if they differ sharply in their historiographic interpretation. This speaks against the contention that understanding of present remains is so irrevocably biased by theoretical and cultural presumptions as to make an objective assessment impossible. (shrink)

Darwin provided us with a powerful theoretical framework to explain the evolution of living systems. Natural selection alone, however, has sometimes been seen as insufficient to explain the emergence of new levels of selection. The problem is one of “circularity” for evolutionary explanations: how to explain the origins of Darwinian properties without already invoking their presence at the level they emerge. That is, how does evolution by natural selection commence in the first place? Recent results in experimental evolution suggest a (...) way forward: Paul Rainey and his collaborators have shown that Darwinian properties could be exogenously imposed via what they call “ecological scaffolding.” This could solve the “black box” dilemma faced by Darwinian explanations of new levels of organization. Yet, despite “scaffolding” recently becoming a popular term in the study of cognition, culture, and evolution, the concept has suffered from vagueness and ambiguity. This article aims to show that scaffolding can be turned into a proper scientific concept able to do explanatory work within the context of the major evolutionary transitions. Doing so will allow us to once again extend the scope of the Darwinian model of evolution by natural selection. (shrink)

In earlier work, I predicted that we would probably not be able to determine the colors of the dinosaurs. I lost this epistemic bet against science in dramatic fashion when scientists discovered that it is possible to draw inferences about dinosaur coloration based on the microstructure of fossil feathers (Vinther et al., 2008). This paper is an exercise in philosophical error analysis. I examine this episode with two questions in mind. First, does this case lend any support to epistemic optimism (...) about historical science? Second, under what conditions is it rational to make predictions about what questions scientists will or will not be able answer? In reply to the first question, I argue that the recent work on the colors of the dinosaurs matters less to the debate about the epistemology of historical science than it might seem. In reply to the second question, I argue that it is difficult to specify a policy that would rule out the failed bet without also being too conservative. (shrink)

We introduce a new type of pluralism about biological function that, in contrast to existing, demonstrates a practical integration among the term’s different meanings. In particular, we show how to generalize Sandra Mitchell’s notion of integrative pluralism to circumstances where multiple epistemic tools of the same type are jointly necessary to solve scientific problems. We argue that the multiple definitions of biological function operate jointly in this way based on how biologists explain the evolution of protein function. To clarify how (...) our account relates to existing views, we introduce a general typology for monist and pluralist accounts along with standardized criteria for judging which is best supported by evidence. (shrink)

The idea that ambiguity can be productive in data science remains controversial. Efforts to make scientific publications and data intelligible to computers generally assume that accommodating multiple meanings for words, known as polysemy, undermines reasoning and communication. This assumption has nonetheless been contested by historians, philosophers, and social scientists, who have applied qualitative research methods to demonstrate the generative and strategic value of polysemy. Recent quantitative results from linguistics have also shown how polysemy can actually improve the efficiency of human (...) communication. I present a new conceptual typology based on a synthesis of prior research about the aims, norms, and circumstances under which polysemy arises and is evaluated. The typology supports a contextual pluralist view of polysemy’s value for scientific research practices: polysemy does both substantial positive and negative work in science, but its utility is context-sensitive in ways that are often overlooked by the norms people have formulated to regulate its use, including prior scholars researching polysemy. I also propose that historical patterns in the use of partial synonyms, i.e. terms with overlapping meanings, provide an especially promising phenomenon for integrative research addressing these issues. (shrink)

In a well-cited book chapter, ecologist Jared Diamond characterizes three main types of experiment performed in community ecology: laboratory experiment, field experiment, and natural experiment. Diamond argues that each form of experiment has strengths and weaknesses, with respect to, for example, realism or the ability to follow a causal trajectory. But does Diamond’s typology exhaust the available kinds of cause-finding practices? Some social scientists have characterized something they call “causal process tracing.” Is this a fourth type of experiment or something (...) else? I examine Diamond’s typology and causal process tracing in the context of a case study concerning the dynamics of wolf and deer populations on the Kaibab Plateau in the 1920s, a case that has been used as a canonical example of a trophic cascade by ecologists but which has also been subject to controversy. I argue that ecologists have profitably deployed causal process tracing together with other types of experiment to help settle questions of causality in this case. It remains to be seen how widespread the use of causal process tracing outside of the social sciences is (or could be), but there are some potentially promising applications, particularly with respect to questions about specific causal sequences. (shrink)

I identify a controversial hypothesis in evolutionary biology called the plasticity-first hypothesis. I argue that the plasticity-first hypothesis is underdetermined and that the most popular means of studying the plasticity-first hypothesis are insufficient to confirm or disconfirm it. I offer a strategy for overcoming this problem. Researchers need to develop a richer middle range theory of plasticity-first evolution that allows them to identify distinctive empirical traces of the hypothesis. They can then use those traces to discriminate between rival explanations of (...) evolutionary episodes. The best tools for developing such a middle range theory are experimental evolution and formal modelling. (shrink)

Social scientists have offered a number of explanations for why Americans commonly deny that human-caused climate change is real. In this paper, I argue that these explanations neglect an important group of climate change deniers: those who say they are on the side of science while also rejecting what they know most climate scientists accept. I then develop a “nature of science” hypothesis that does account for this group of deniers. According to this hypothesis, people have serious misconceptions about what (...) scientific inquiry ought to look like. Their misconceptions interact with partisan biases to produce denial of human-caused climate change. After I develop this hypothesis, I propose ways of confirming that it is true. Then I consider its implications for efforts to combat climate change denial and for other cases of public rejection of science. (shrink)

Despite wide recognition that speculation is critical for successful science, philosophers have attended little to it. When they have, speculation has been characterized in narrowly epistemic terms: a hypothesis is speculative due to its (lack of) evidential support. These ‘evidence-first’ accounts provide little guidance for what makes speculation productive or egregious, nor how to foster the former while avoiding the latter. I examine how scientists discuss speculation and identify various functions speculations play. On this basis, I develop a ‘function-first’ account (...) of speculation. This analysis grounds a richer discussion of when speculation is egregious and when it is productive, based in both fine-grained analysis of the speculation’s purpose, and what I call the ‘epistemic situation’ scientists face. (shrink)

Debate about the epistemic prowess of historical science has focused on local underdetermination problems generated by a lack of historical data; the prevalence of information loss over geological time, and the capacities of scientists to mitigate it. Drawing on Leonelli’s recent distinction between ‘phenomena-time’ and ‘data-time’ I argue that factors like data generation, curation and management significantly complexifies and undermines this: underdetermination is a bad way of framing the challenges historical scientists face. In doing so, I identify circumstances of epistemic (...) scarcity where underdetermination problems are particularly salient, and discuss cases where legacy data—data generated using differing technologies and systems of practice—are drawn upon to overcome underdetermination. This suggests that one source of overcoming underdetermination is our knowledge of science’s past. Further, data-time makes agnostic positions about the epistemic fortunes of scientists working under epistemic scarcity more plausible. But agnosticism seems to leave philosophers without much normative grip. So, I sketch an alternative approach: focusing on the strategies scientists adopt to maximize their epistemic power in light of the resources available to them. (shrink)

Paleobiologists often provide simple narratives to explain complex, contingent episodes. These narratives are sometimes ‘one-shot hypotheses’ which are treated as being mutually exclusive with other possible explanations of the target episode, and are thus extended to accommodate as much about the episode as possible. I argue that a provisional preference for such hypotheses provides two kinds of productive scaffolding. First, they generate ‘hypothetical difference-makers’: one-shot hypotheses highlight and isolate empirically tractable dependencies between variables. Second, investigations of hypothetical difference-makers provision explanatory (...) resources, the ‘raw materials’ for constructing more complex—and likely more adequate—explanations. Provisional preferences for simple, one-shot hypotheses in historical science, then, is defeasibly justified on indirect—strategic—grounds. My argument is made in reference to recent developments regarding the K–Pg extinction. (shrink)

Both paleobiology and investigations of ‘major evolutionary transitions’ are intimately concerned with the macroevolutionary shape of life. It is surprising, then, how little studies of major transitions are informed by paleontological perspectives and. I argue that this disconnect is partially justified because paleobiological investigation is typically ‘phenomena-led’, while investigations of major transitions are ‘theory-led’. The distinction turns on evidential relevance: in the former case, evidence is relevant in virtue of its relationship to some phenomena or hypotheses concerning those phenomena; in (...) the latter, evidence is relevant in virtue of providing insights into, or tests of, an abstract body of theory. Because paleobiological data is by-and-large irrelevant to the theory which underwrites the traditional conception of major transitions, it is of limited use to that research program. I suggest that although the traditional conception of major transitions is neither ad-hoc or problematically incomplete, its promise of providing unificatory explanations of the transitions is unlikely to be kept. Further, examining paleobiological investigations of mass extinctions and organogenesis, I further argue that whether or not transitions in paleobiology count as ‘major’ turns on how we conceive of major transitions ; although major transitions potentially have a unified theoretical basis, recent developments suggest that investigations are becoming increasingly phenomena-led; adopting phenomena-led investigations maximizes the evidence available to paleobiologists. (shrink)

We argue that narratives are central to the success of historical reconstruction. Narrative explanation involves tracing causal trajectories across time. The construction of narrative, then, often involves postulating relatively speculative causal connections between comparatively well-established events. But speculation is not always idle or harmful: it also aids in overcoming local underdetermination by forming scaffolds from which new evidence becomes relevant. Moreover, as our understanding of the past’s causal milieus become richer, the constraints on narrative plausibility become increasingly strict: a narrative’s (...) admissibility does not turn on mere logical consistency with background data. Finally, narrative explanation and explanation generated by simple, formal models complement one another. Where models often achieve isolation and precision at the cost of simplification and abstraction, narratives can track complex changes in a trajectory over time at the cost of simplicity and precision. In combination both allow us to understand and explain highly complex historical sequences. (shrink)

Cognitive archaeologists infer from material remains to the cognitive features of past societies. We characterize cognitive archaeology in terms of trace-based reasoning, which in the case of cognitive archaeology involves inferences drawing upon background theory linking objects from the archaeological record to cognitive features. We analyse such practices, examining work on cognitive evolution, language, and musicality. We argue that the central epistemic challenge for cognitive archaeology is often not a paucity of material remains, but insufficient constraint from cognitive theories. However, (...) we also argue that the success of cognitive archaeology does not necessarily require well-developed cognitive theories: Success might instead lead to them. (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)

Ethnographic analogy, the use of comparative data from anthropology to inform reconstructions of past human societies, has a troubled history. Archaeologists often express concern about, or outright reject, the practice—and sometimes do so in problematically general terms. This is odd, as the use of comparative data in archaeology is the same pattern of reasoning as the ‘comparative method’ in biology, which is a well-developed and robust set of inferences which play a central role in discovering the biological past. In pointing (...) out this continuity, I argue that there is no ‘special pleading’ on the part of archaeologists in this regard: biologists must overcome analogous epistemic difficulties in their use of comparative data. I then go on to emphasize the local, empirically tractable ways in which particular ethnographic analogies may be licensed. (shrink)

Philosophers have usually highlighted how the weakness and paucity of historical evidence underdetermine the choice between rival historical explanations. Focusing underdetermination on the link between theory and evidence comes, I argue, with three assumptions: competing hypotheses are easy to generate, investigators agree on the constitution and interpretation of the evidence and a plurality of hypotheses is a useful evil to reach consensus. The last assumption implies that the sustained coexistence of incompatible hypotheses is considered as a scientific failure. I argue (...) that this negative vision of sustained disagreement has monistic undertones. By drawing from a case study in evolutionary biology, this paper defends a form of scientific pluralism. Firstly, I show that underdetermination is not only found at the inferential level but also at the level of the constitution and interpretation of the evidence, on the choice of investigative scaffolds and when interpreting background theories. Because of that, competing hypotheses exhibit a degree of methodological incommensurability. While catastrophic from a monistic standpoint, I defend that scientific pluralism gives a different, and I think richer, account of such situations. On the plus side, competing approaches benefit from their sustained coexistence and interaction. I argue that this generates direct and indirect epistemic goods independently of whether the controversy is solved. Scientific pluralism also shifts our attention from achieving consensus to managing disagreement. The challenge becomes to maintain the conditions for fruitful interactions in a community with incommensurable approaches and heterogeneous expertise. (shrink)

This article is a study of the role and use of evidence in the evaluation of claims in the historical sciences. In order to do this, I develop a “snapshot” approach to Toulmin schemas. This framework is applied to the case of Archezoa, an initially supported then eventually rejected hypothesis in evolutionary biology. From this case study, I criticize Cleland’s “smoking gun” account of the methodology of the historical sciences. I argue that Toulmin schemas are conceptually precise tools that allow (...) for the building of enriched reconstructions of evidential reasoning. From the application of this framework, I discuss three ways in which the construction and use of facts in the historical sciences are theory-laden. Despite its inherent limits, TS are heuristically useful tools to identify epistemic moves that could be further investigated. It also sheds light on the positive roles of speculation in the historical sciences. Finally, I argue that it provides a context-specific and individuated understanding of hypothesis evaluation in the historical sciences. Overall, I think the application of Toulmin schemas to cases of evidential reasoning in the historical sciences is a promising descriptive and heuristic tool for philosophers of science. (shrink)

The epidemiologist Bradford Hill famously argued that in epidemiology, specificity of association (roughly, the fact that an environmental or behavioral risk factor is associated with just one or at most a few medical outcomes) is strong evidence of causation. Prominent epidemiologists have dismissed Hill’s claim on the ground that it relies on a dubious `one-cause one effect’ model of disease causation. The paper examines this methodological controversy, and argues that specificity considerations do have a useful role to play in causal (...) inference in epidemiology. More precisely, I argue that specificity considerations help solve a pervasive inferential problem in contemporary epidemiology: the problem of determining whether an exposure-outcome correlation might be due to confounding by a social factor. This examination of specificity has interesting consequences for our understanding of the methodology of epidemiology. It highlights how the methodology of epidemiology relies on local tools designed to address specific inference problems peculiar to the discipline, and shows that observational causal inference in epidemiology can proceed with little prior knowledge of the causal structure of the phenomenon investigated. I also argue that specificity of association cannot (despite claims to the contrary) be entirely explained in terms of Woodward’s well-known concept of “one-to-one” causal specificity. This is because specificity as understood by epidemiologists depends on whether an exposure (or outcome) is associated with a `heterogeneous’ set of variables. This dimension of heterogeneity is not captured in Woodward’s notion, but is crucial for understanding the evidential import of specificity of association. (shrink)

Pluralism about scientific method is more-or-less accepted, but the consequences have yet to be drawn out. Scientists adopt different methods in response to different epistemic situations: depending on the system they are interested in, the resources at their disposal, and so forth. If it is right that different methods are appropriate in different situations, then mismatches between methods and situations are possible. This is most likely to occur due to method bias: when we prefer a particular kind of method, despite (...) that method clashing with evidential context or our aims. To explore these ideas, we sketch a kind of method pluralism which turns on two properties of evidence, before using agent-based models to examine the relationship between methods, epistemic situations, and bias. Based on our results, we suggest that although method bias can undermine the efficiency of a scientific community, it can also be productive through preserving a diversity of evidence. We consider circumstances where method bias could be particularly egregious, and those where it is a potential virtue, and argue that consideration of method bias reveals that community standards deserve a central place in the epistemology of science. (shrink)