Discovery proceeds in stages of construction, evaluation, and revision. Each of these stages is constrained by what is known or conjectured about what is being discovered. A new characterization of mechanism aids in specifying what is to be discovered when a mechanism is sought. Guidance in discovering mechanisms may be provided by the reasoning strategies of schema instantiation, modular subassembly, and forward/backward chaining. Examples are found in mechanisms in molecular biology, biochemistry, immunology, and evolutionary biology.

Professionals often believe that they must “exercise judgment” in making decisions critical to other people’s lives. The relative superiority of statistical prediction rules to intuitive judgment for combining incomparable sources of information to predict important human outcomes leads us to question this personal input belief. Some professionals hence use SPR’s to “educate” intuitive judgment, rather than replace it. In psychology in particular, such amalgamation is not justified. If a well‐validated SPR that is superior to professional judgment exists in a relevant (...) decision making context, professionals should use it, totally absenting themselves from the prediction. (shrink)

This paper attacks the perennial philosophical and scientific quest for a simple and unified vision of the world. Without denying the attraction of this vision, I argue that such a goal often seriously distorts our understanding of complex phenomena. The argument is illustrated with reference to simplistic attempts to provide extremely general views of biology, and especially of human nature, through the theory of evolution. Although that theory is a fundamental ingredient of our scientific world view, it provides only one (...) of a number of perspectives that are required for an understanding of biology in general, and human behaviour in paticular. The argument is connected to the replacement of views of science in terms of universal laws with views that emphasise ranges of models more locally suited to specific phenomena. (shrink)

We tend to think that there are different types of biological taxa: some taxa are species, others are genera, while others are families. Linnaeus gave us his ranks in 1731. Biological theory has changed since Linnaeus’s time. Nevertheless, the vast majority of biologists still assign Linnaean ranks to taxa, even though that practice is at odds with evolutionary theory and even though it causes a number of practical problems. The Linnaean ranks should be abandoned and alternative methods for displaying the (...) hierarchical relations of taxa should be adopted. (shrink)

More powerful methods for studying and integrating the historical track record of scientific episodes and scientific judgment, or what Faust and Meehl describe as a program of meta‐science and meta‐scientific studies, can supplement and extend more commonly used case study methods. We describe the basic premises of meta‐science, overview methodological considerations, and provide examples of meta‐scientific studies. Meta‐science can help to clarify or resolve long‐standing questions in the history and philosophy of science and provide practical help to the working scientist.

What has science actually achieved? A theory of achievement should define what has been achieved, describe the means or methods used in science, and explain how such methods lead to such achievements. Predictive accuracy is one truth‐related achievement of science, and there is an explanation of why common scientific practices tend to increase predictive accuracy. Akaike’s explanation for the success of AIC is limited to interpolative predictive accuracy. But therein lies the strength of the general framework, for it also provides (...) a clear formulation of many open problems of research. (shrink)

Philosophers of science typically associate the causal-mechanical view of scientific explanation with the work of Railton and Salmon. In this paper I shall argue that the defects of this view arise from an inadequate analysis of the concept of mechanism. I contrast Salmon's account of mechanisms in terms of the causal nexus with my own account of mechanisms, in which mechanisms are viewed as complex systems. After describing these two concepts of mechanism, I show how the complex-systems approach avoids certain (...) objections to Salmon's account of causal-mechanical explanation. I conclude by discussing how mechanistic explanations can provide understanding by unification. (shrink)

An interpretation of John Dewey’s views about realism, science, and naturalistic philosophy is presented. Dewey should be seen as an unorthodox realist, with respect to both general metaphysical debates about realism and with respect to debates about the aims and achievements of science.

A different way of thinking about how the sciences are organized is suggested by the use of cross‐disciplinary computational methods as the organizing unit of science, here called computational templates. The structure of computational models is articulated using the concepts of construction assumptions and correction sets. The existence of these features indicates that certain conventionalist views are incorrect, in particular it suggests that computational models come with an interpretation that cannot be removed as well as a prior justification. A form (...) of selective realism is described which denies that one can simply read the ontological commitments from the theory itself. (shrink)

The idea that rational agents should have acyclic preferences and should obey conditionalization has been defended on the grounds that otherwise an agent is threatened with becoming a “money pump.” This essay argues that such arguments fail to prove their claims.

I consider the question of how literally one can construe the “gauge argument,” which is the canonical means of understanding the putatively central import of local gauge symmetry principles for fundamental physics. As I argue, the gauge argument must be afforded a heuristic reading. Claims to the effect that the argument reflects a deep “logic of nature” must, for numerous reasons I discuss, be taken with a grain of salt.

A model of inductive inquiry is defined within the context of first‐order logic. The model conceives of inquiry as a game between Nature and a scientist. To begin the game, a nonlogical vocabulary is agreed upon by the two players, along with a partition of a class of countable structures for that vocabulary. Next, Nature secretly chooses one structure from some cell of the partition. She then presents the scientist with a sequence of facts about the chosen structure. With each (...) new datum the scientist announces a guess about the cell to which the chosen structure belongs. To succeed in his or her inquiry, the scientist’s successive conjectures must be correct all but finitely often, that is, the conjectures must converge in the limit to the correct cell. Different kinds of scientists can be investigated within this framework. At opposite ends of the spectrum are dumb scientists that rely on the strategy of “induction by enumeration,” and smart scientists that rely on an operator of belief revision. We report some results about the scope and limits of these two inductive strategies. (shrink)

The Akaike Information Criterion can be a valuable tool of scientific inference. This statistic, or any other statistical method for that matter, cannot, however, be the whole of scientific methodology. In this paper some of the limitations of Akaikean statistical methods are discussed. It is argued that the full import of empirical evidence is realized only by adopting a richer ideal of empirical success than predictive accuracy, and that the ability of a theory to turn phenomena into accurate, agreeing measurements (...) of causally relevant parameters contributes to the evidential support of the theory. This is illustrated by Newton's argument from orbital phenomena to the inverse-square law of gravitation. (shrink)

1. The Physical Church-Turing Thesis. Physicists often interpret the Church-Turing Thesis as saying something about the scope and limitations of physical computing machines. Although this was not the intention of Church or Turing, the Physical Church Turing thesis is interesting in its own right. Consider, for example, Wolfram’s formulation: One can expect in fact that universal computers are as powerful in their computational capabilities as any physically realizable system can be, that they can simulate any physical system . . . (...) No physically implementable procedure could then shortcut a computationally irreducible process. (Wolfram 1985) Wolfram’s thesis consists of two parts: (a) Any physical system can be simulated (to any degree of approximation) by a universal Turing machine (b) Complexity bounds on Turing machine simulations have physical significance. For example, suppose that the computation of the minimum energy of some system of n particles takes at least exponentially (in n) many steps. Then the relaxation time of the actual physical system to its minimum energy state will also take exponential time. (shrink)

This essay examines logical empiricism and American pragmatism, arguing that American philosophy's embrace of logical empiricism in the 1930s was not a turning away from Dewey's pragmatism. It places both movements within scientific philosophy and finds two key points on which they agreed: their revolutionary ambitions and their social engineering sensibility. The essay suggests that the disagreement over emotivism in ethics should be placed within the context of a larger issue on which the movements disagreed: demarcationism and imperialism.

It has long been known that the practice of testing all hypotheses at the same level , regardless of the distribution of the data, is not consistent with Bayesian expected utility maximization. According to de Finetti’s “Dutch Book” argument, procedures that are not consistent with expected utility maximization are incoherent and they lead to gambles that are sure to lose no matter what happens. In this paper, we use a method to measure the rate at which incoherent procedures are sure (...) to lose, so that we can distinguish slightly incoherent procedures from grossly incoherent ones. We present an analysis of testing a simple hypothesis against a simple alternative as a case‐study of how the method can work. (shrink)

We show how Richard Jeffrey’s The Logic of Decision provides the proper formalism for calculating expected fitness for correlated encounters in general. As an illustration, some puzzles about kin selection are resolved.

Akaike’s framework for thinking about model selection in terms of the goal of predictive accuracy and his criterion for model selection have important philosophical implications. Scientists often test models whose truth values they already know, and they often decline to reject models that they know full well are false. Instrumentalism helps explain this pervasive feature of scientific practice, and Akaike’s framework helps provide instrumentalism with the epistemology it needs. Akaike’s criterion for model selection also throws light on the role of (...) parsimony considerations in hypothesis evaluation. I explain the basic ideas behind Akaike’s framework and criterion; several biological examples, including the use of maximum likelihood methods in phylogenetic inference, are considered. (shrink)

This paper presents a counterfactual account of what a mechanism is. Mechanisms consist of parts, the behavior of which conforms to generalizations that are invariant under interventions, and which are modular in the sense that it is possible in principle to change the behavior of one part independently of the others. Each of these features can be captured by the truth of certain counterfactuals.

Evidence-Based Medicine is a relatively new movement that seeks to put clinical med- icine on a firmer scientific footing. I take it as uncontroversial that medical practice should be based on best evidence-the interesting questions concern the details. This paper tries to move towards a coherent and unified account of best evidence in medicine, by exploring in particular the EBM position on RCTs (randomized controlled trials).

Scientific models may be more useful for false assumptions they make than true ones when one is interested not in the fit of the model, but in the form of the residuals. Modeling Darwin’s “blending” theory of inheritance shows how it illuminates features of Mendelian theory. Insufficient understanding of it leads to incorrect moves in modeling population structure. But it may prove even more useful for organizing a theory of cultural evolution. Analysis of “blending” inheritance gives new tools for recognizing (...) population structure for culture and for understanding differences between biological and cultural inheritance. (shrink)

Phylogenetic information is often necessary to distinguish between evolutionary scenarios. Recently, some prominent proponents of evolutionary psychology have acknowledged this, and have claimed that such evidence has in fact been brought to bear on adaptive hypotheses involving complex human psychological traits. Were this possible, it would be a valuable source of evidence regarding hypothesized adaptive traits in humans. However, the structure of the Hominidae family makes this difficult or impossible. For many traits of interest, the closest extant relatives to the (...) human species are too phenotypically different from humans for such methods to provide meaningful data. While phylogenetic information can be useful for testing adaptive hypotheses in humans, these generally involve traits that are (a) not widely shared in the species or (b) fairly widely shared in the Hominidae family, and hence likely of a lower order of complexity than the sorts of traits evolutionary psychology has so far been interested in. (shrink)