I contrast our own evidence for the hypothesis of organic fossil origins with that available in previous centuries, suggesting that the most powerful contemporary evidence consists in a form of projective support whose distinctive features are not well captured by familiar hypothetico-deductive, abductive, or even more recent and more technically sophisticated accounts of scientific confirmation. I suggest that such accounts either misrepresent or ignore something important about the heterogeneous ways in which scientific hypotheses can be supported by evidence, and I (...) go on to suggest that the search for any single such account may be misguided in any case. (shrink)

One of the most interesting challenges facing paleobiologists is explaining the Cambrian explosion, the dramatic appearance of most metazoan animal phyla in the Early Cambrian, and the subsequent stability of these body plans over the ensuing 530 million years. We propose that because phenotypic variation decreases through geologic time, because microRNAs (miRNAs) increase genic precision, by turning an imprecise number of mRNA transcripts into a more precise number of protein molecules, and because miRNAs are continuously being added to metazoan genomes (...) through geologic time, miRNAs might be instrumental in the canalization of development. Further, miRNAs ultimately allow for natural selection to elaborate morphological complexity, because by reducing gene expression variability, miRNAs increase heritability, allowing selection to change characters more effectively. Hence, miRNAs might play an important role in shaping metazoan macroevolution, and might be part of the solution to the Cambrian conundrum. (shrink)

It is customary to distinguish experimental from purely observational sciences. The former include physics and molecular biology, the latter astronomy and palaeontology. Experiments involve actively intervening in the course of nature, as opposed to observing events that would have happened anyway. When a molecular biologist inserts viral DNA into a bacterium in his laboratory, this is an experiment; but when an astronomer points his telescope at the heavens, this is an observation. Without the biologist’s handiwork the bacterium would never have (...) contained foreign DNA; but the planets would have continued orbiting the sun whether or not the astronomer had directed his telescope skyward. The observational/experimental distinction would probably be difficult to make precise 1, as the notion of an ‘intervention’ is not easily defined, but it is intuitively fairly clear, and is frequently invoked by scientists and historians of science. Experimentation, or ‘putting questions to nature’, is often cited as a hallmark of the modern scientific method, something that permitted the enormous advances of the last 350 years. And it is sometimes said that the social sciences lag behind the natural because controlled experiments cannot be done so readily in the former. Moreover in certain sciences, e.g. epidemiology, students are explicitly taught that experimental data is preferable to observational data, particularly for doing causal inference. So the distinction between observational and experimental science has quite wide currency, and is often regarded as methodologically significant. Surprisingly, mainstream philosophy of science has had rather little to say about the observational/experimental distinction. 2 For example, discussions of confirmation usually invoke a notion of ‘evidence’, to be contrasted with ‘theory’ or ‘hypothesis’; the aim is to understand how the evidence bears on the hypothesis. But whether this ‘evidence’ comes from observation or experiment generally plays no role in the discussion; this is true …. (shrink)

This article explores the characteristics of research sites that scientists have called “natural experiments” to understand and develop usable distinctions for the social sciences between “Nature’s or Society’s experiments” and “natural experiments.” In this analysis, natural experiments emerge as the retro-fitting by social scientists of events that have happened in the social world into the traditional forms of field or randomized trial experiments. By contrast, “Society’s experiments” figure as events in the world that happen in circumstances that are already sufficiently (...) “controlled” to be open for direct analysis without reconstruction work. (shrink)

Many biological investigations are organized around a small group of species, often referred to as ‘model organisms’, such as the fruit fly Drosophila melanogaster. The terms ‘model’ and ‘modelling’ also occur in biology in association with mathematical and mechanistic theorizing, as in the Lotka–Volterra model of predator-prey dynamics. What is the relation between theoretical models and model organisms? Are these models in the same sense? We offer an account on which the two practices are shown to have different epistemic characters. (...) Theoretical modelling is grounded in explicit and known analogies between model and target. By contrast, inferences from model organisms are empirical extrapolations. Often such extrapolation is based on shared ancestry, sometimes in conjunction with other empirical information. One implication is that such inferences are unique to biology, whereas theoretical models are common across many disciplines. We close by discussing the diversity of uses to which model organisms are put, suggesting how these relate to our overall account. 1 Introduction2 Volterra and Theoretical Modelling3 Drosophila as a Model Organism4 Generalizing from Work on Model Organisms5 Phylogenetic Inference and Model Organisms6 Further Roles of Model Organisms6.1 Preparative experimentation6.2 Model organisms as paradigms6.3 Model organisms as theoretical models6.4 Inspiration for engineers6.5 Anchoring a research community7 Conclusion. (shrink)

The historical sciences, such as geology, evolutionary biology, and archaeology, appear to have no means to test hypotheses. However, on closer examination, reasoning in the historical sciences relies upon regularities, regularities that can be tested. I outline the role of regularities in the historical sciences, and in the process, blur the distinction between the historical sciences and the experimental sciences: all sciences deploy theories about the world in their investigations.

Geologists, Paleontologists and other historical scientists are frequently concerned with narrative explanations targeting single cases. I show that two distinct explanatory strategies are employed in narratives, simple and complex. A simple narrative has minimal causal detail and is embedded in a regularity, whereas a complex narrative is more detailed and not embedded. The distinction is illustrated through two case studies: the ‘snowball earth’ explanation of Neoproterozoic glaciation and recent attempts to explain gigantism in Sauropods. This distinction is revelatory of historical (...) science. I argue that at least sometimes which strategy is appropriate is not a pragmatic issue, but turns on the nature of the target. Moreover, the distinction reveals a counterintuitive pattern of progress in some historical explanation: shifting from simple to complex. Sometimes, historical scientists rightly abandon simple, unified explanations in favour of disunified, complex narratives. Finally I compare narrative and mechanistic explanation, arguing that mechanistic approaches are inappropriate for complex narrative explanations. (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)

Experimental research is commonly held up as the paradigm of "good" science. Although experiment plays many roles in science, its classical role is testing hypotheses in controlled laboratory settings. Historical science is sometimes held to be inferior on the grounds that its hypothesis cannot be tested by controlled laboratory experiments. Using contemporary examples from diverse scientific disciplines, this paper explores differences in practice between historical and experimental research vis-à-vis the testing of hypotheses. It rejects the claim that historical research is (...) epistemically inferior. For as I argue, scientists engage in two very different patterns of evidential reasoning and, although there is overlap, one pattern predominates in historical research and the other pattern predominates in classical experimental research. I show that these different patterns of reasoning are grounded in an objective and remarkably pervasive time asymmetry of nature. (shrink)

This chapter is concerned with the Cambrian explosion. It considers only one particular kind of explanation for the Cambrian radiation: that major innovations in animal body plan were produced from relatively few genetic changes of large phenotypic effect. It investigates the developmental genetic hypothesis of the origin and maintenance of body plans. This chapter suggests that the genetic architecture underlying body plans was not set during the Cambrian and has been immutable since. It shows that the link between body plan (...) and phylum can become blurry when the minor phyla are considered. (shrink)

Manipulablity theories of causation, according to which causes are to be regarded as handles or devices for manipulating effects, have considerable intuitive appeal and are popular among social scientists and statisticians. This article surveys several prominent versions of such theories advocated by philosophers, and the many difficulties they face. Philosophical statements of the manipulationist approach are generally reductionist in aspiration and assign a central role to human action. These contrast with recent discussions employing a broadly manipulationist framework for understanding causation, (...) such as those due to the computer scientist Judea Pearl and others, which are non-reductionist and rely instead on the notion of an intervention. This is simply an appropriately exogenous causal process; it has no essential connection with human action. This interventionist framework manages to avoid at least some of these difficulties faced by traditional philosophical versions of the manipulability theory and helps to clarify the content of causal claims. (shrink)