This book examines the philosophical conception of abductive reasoning as developed by Charles S. Peirce, the founder of American pragmatism. It explores the historical and systematic connections of Peirce's original ideas and debates about their interpretations. Abduction is understood in a broad sense which covers the discovery and pursuit of hypotheses and inference to the best explanation. The analysis presents fresh insights into this notion of reasoning, which derives from effects to causes or from surprising observations to explanatory theories. The (...) author outlines some logical and AI approaches to abduction as well as studies various kinds of inverse problems in astronomy, physics, medicine, biology, and human sciences to provide examples of retroductions and abductions. The discussion covers also everyday examples with the implication of this notion in detective stories, one of Peirce’s own favorite themes. The author uses Bayesian probabilities to argue that explanatory abduction is a method of confirmation. He uses his own account of truth approximation to reformulate abduction as inference which leads to the truthlikeness of its conclusion. This allows a powerful abductive defense of scientific realism. This up-to-date survey and defense of the Peircean view of abduction may very well help researchers, students, and philosophers better understand the logic of truth-seeking. (shrink)

Intelligent design theorists assert that ID is a scientific theory that is merely consistent with some religious beliefs. Many critics point to the circumstantial evidence of the apparent development of ID from creation science and the affiliation of ID with mainstream evangelical organizations to assert its religious orientation. This article suggests that the position of ID proponents is a substantial understatement, and that beyond the circumstantial evidence of critics, fundamental Christian doctrine constitutes the essence of ID theory. The bulk of (...) scholarship on ID is polarized into those for and against, as most focus on adjudicating ID truth claims, but this adversarial structure elides some important complexities. This article sets aside the truth claims of ID and focuses more broadly on the discourse in which it is situated to show the Christian core of ID and to examine several hallmarks of religion apparent from this perspective. (shrink)

Intelligent Design creationism is often criticized for failing to be science because it falls afoul of some demarcation criterion between science and non-science. This paper argues that this objection to Intelligent Design is misplaced because it assumes that a consistent non-theological characterization of Intelligent Design is possible. In contrast, it argues that, if Intelligent Design is taken to be non-theological doctrine, it is not intelligible. Consequently, a demarcation criterion cannot be used to judge its status. This position has the added (...) advantage of providing reasons to reject Intelligent Design creationism without invoking potentially philosophically controversial demarcation criteria. (shrink)

Since the late 1990s, the characterization of complete DNA sequences for a large and taxonomically diverse set of species has continued to gain in speed and accuracy. Sequence analyses have indicated a strikingly baroque structure for most eukaryotic genomes, with multiple repeats of DNA sequences and with very little of the DNA specifying proteins. Much of the DNA in these genomes has no known function. These results have generated strong interest in the factors that govern the evolution of genome architecture. (...) While adaptationist ‘just so’ stories have been offered, recent theoretical analyses based on mathematical population genetics strongly suggest that non-adaptive processes dominate genome architecture evolution. This article critically synthesizes and develops these arguments, explicating a core argument along with several variants. It provides a critical assessment of the evidence that supports these arguments’ premises. It also analyses adaptationist responses to these arguments and notes potential problems with the core argument. These theoretical analyses continue the molecular reinterpretation of evolution initiated by the neutral theory in 1968. The article ends by noting that some of these arguments can also be extended to evolution at higher levels of organization which raises questions about adaptationism in general. This remains a puzzle because there is probably little reason to doubt that many organismic features are genuine adaptations. 1 Introduction2 Preliminaries: Senses of Adaptationism3 Genome Architecture3.1 Surprises of early eukaryotic genetics3.2 Genome structure, post-20014 The Case against Adaptationism4.1 Just so stories versus population genetics4.2 The core argument4.3 Three variants of the core argument4.4 Examples: Non-adaptive features of the genome5 Adaptationist Responses6 Concluding Remarks. (shrink)

This response to Sober's (2008) Evidence and Evolution draws out and criticizes some consequences of his analysis because of its reliance on a likelihood framework for adjucating the dispute between (Intelligent Design) creationism and evolution. In particular, Sober's analysis does not allow it to be formally claimed that evolutionary theory better explains living phenomena than Intelligent Design and makes irrelevant the contribution of the theory of evolution by natural selection to assessments of the status of the argument from design. Finally, (...) a rudimentary alternative framework for theory confirmation is presented here which avoids these conclusions by rejecting likelihoodism and deploying multiple criteria to the problem of scientific theory choice. (shrink)

Two questions are raised for Grafen’s formal darwinism project of aligning evolutionary dynamics under natural selection with the optimization of phenotypes for individuals of a population. The first question concerns mean fitness maximization during frequency-dependent selection; in such selection regimes, not only is mean fitness typically not maximized but it is implausible that any parameter closely related to fitness is being maximized. The second question concerns whether natural selection on inclusive fitness differences can be regarded as individual selection or whether (...) it leads to a departure from the central motivation that led to the formal darwinism project, viz., to show that “Darwinian” evolution through individual selection leads to “good design” or phenotypic adaptation through trait optimization. (shrink)

This paper reconstructs the history of the introduction and use of iterative algorithms in conservation biology in the 1980s and early 1990s in order to prioritize areas for protection as nature reserves. The importance of these algorithms was that they led to greater economy in spatial extent (“efficiency”) in the selection of areas to represent biological features adequately (that is, to a specified level) compared to older methods of scoring and ranking areas using criteria such as biotic “richness” (the number (...) of features of interest). The development of these algorithms was critical to producing a research program for conservation biology that was distinct from ecology and eventually led to what came to be called systematic conservation planning. Very similar algorithmic approaches were introduced independently in the 1980–1990 period in Australia, South Africa, and (arguably) the United Kingdom. The key rules in these algorithms were the use of rarity and what came to be called complementarity (the number of new or under-represented features in an area relative to those that had already been selected). Because these algorithms were heuristic, they were not guaranteed to produce optimal (most “efficient”) solutions. However, complementarity came to be seen as a principle rather than a rule in an algorithm and its use was also advocated for the former reason. Optimal solutions could be produced by reformulating the reserve selection problem in a mathematical programming formalism and using exact algorithms developed in that context. A dispute over the relevance of full optimality arose and was never resolved. Moreover, exact algorithms could not easily incorporate criteria determining the spatial configuration of networks of selected areas, in contrast to heuristic algorithms. Meanwhile metaheuristic algorithms emerged in the 1990s and came to be seen as a credible more effective alternative to the heuristic algorithms. Ultimately what was important about these developments was that the reserve selection problem came to be viewed a complex optimal decision problem under uncertainty, resource, and other constraints. It was a type of problem that had no antecedent in traditional ecology. (shrink)

Controversy over the possibility of detecting design in natural sciences: According to intelligent design theory, certain biological and cosmic phenomena are designed by an intelligent being and this design is scientifically detectable. However, critics refuse to regard this theory as scientific, thereby suggesting that it does not deserve serious discussion in scientific circles. The article presents main methodological objections to intelligent design theory, indicating its unscientific or pseudoscientific character and impossibility of scientific design detection. Critics try to show that this (...) theory: 1) violates the principle of methodological naturalism ; 2) is empirically untestable; 3) it does not invoke natural laws, says nothing about the designer and the designing mechanism; 4) it does not offer predictions; 5) it is an argument from ignorance, and 6) it does not lead to fruitful research program and hence is not useful for science. These objections will be analyzed from the perspective of methodological thesis of design theorists that the sufficient condition of design inference are the characteristic effects leaved by the activity of the designer, which indicate the final cause, although they do not have to be the basis for determining the designer’s identity. If this thesis is sound, then the objections that intelligent design theory is not scientific are rebutted or weakened. Moreover, it turns out that, basically, detecting design of supernatural beings does not differ from detecting design of natural beings. For that reason, there is no qualitative difference between these two procedures and both can be regarded as scientific. (shrink)

The argument that the second law of thermodynamics contradicts the theory of evolution has recently been revived by anti-evolutionists. In its basic form, the argument asserts that whereas evolution implies that there has been an increase in biological complexity over time, the second law, a fundamental principle of physics, shows this to be impossible. Scientists have responded primarily by noting that the second law does not rule out increases in complexity in open systems, and since the Earth receives energy from (...) the Sun, it is an open system. This reply is correct as far as it goes, and it adequately rebuts the most crude versions of the second law argument. However, it is insufficient against more sophisticated versions, and it leaves many relevant aspects of thermodynamics unexplained. We shall consider the history of the argument, explain the nuances various anti-evolution writers have brought to it, and offer thorough explanations for why the argument is fallacious. We shall emphasize in particular that the second law is best viewed as a mathematical statement. Since anti-evolutionists never make use of the mathematical structure of thermodynamics, invocations of the second law never contribute anything substantive to their discourse. (shrink)

The teaching of evolution in American high schools has long been a source of controversy. The past decade has seen an important shift in the rhetoric of anti-evolutionists, toward arguments of a strongly mathematical character. These mathematical arguments, while different in their specifics, follow the same general program and rely on the same underlying model of evolution. We shall discuss the nature and history of this program and model and describe general reasons for skepticism with regard to any anti-evolutionary arguments (...) based upon them. We shall then survey the major arguments used by anti-evolutionists, to show how our general considerations make it possible to quickly identify their weakest points. (shrink)

A variety of different arguments have been offered for teaching ‘‘both sides’’ of the evolution/ID debate in public schools. This article reviews five of the most common types of arguments advanced by proponents of Intelligent Design and demonstrates how and why they are founded on confusion and misunderstanding. It argues on behalf of teaching evolution, and relegating discussion of ID to philosophy or history courses.

Dissent is thought to play a valuable role in science, so that scientific communities ought to create opportunities for receiving critical feedback and take dissenting views seriously. There is concern, however, that some dissent does more harm than good. Dissent on climate change and evolutionary theory, for example, has confused the public, created doubt about existing consensus, derailed public policy, and forced scientists to devote resources to respond. Are there limits to the extent to which scientific communities have obligations to (...) seek and engage dissenting views? We consider the two main criteria that have been offered for what constitutes “normatively appropriate dissent” or the sort of dissent that ought to have the opportunity to be heard and taken seriously. Many have argued that dissenters must (1) engage in uptake of criticism against their own views and (2) share some standards for theory appraisal. We argue these criteria ultimately are unsuccessful. (shrink)

In recent controversies about Intelligent Design Creationism (IDC), the principle of methodological naturalism (MN) has played an important role. In this paper, an often neglected distinction is made between two different conceptions of MN, each with its respective rationale and with a different view on the proper role of MN in science. According to one popular conception, MN is a self-imposed or intrinsic limitation of science, which means that science is simply not equipped to deal with claims of the supernatural (...) (Intrinsic MN or IMN). Alternatively, we will defend MN as a provisory and empirically grounded attitude of scientists, which is justified in virtue of the consistent success of naturalistic explanations and the lack of success of supernatural explanations in the history of science (Provisory MN or PMN). Science does have a bearing on supernatural hypotheses, and its verdict is uniformly negative. We will discuss five arguments that have been proposed in support of IMN: the argument from the definition of science, the argument from lawful regularity, the science stopper argument, the argument from procedural necessity, and the testability argument. We conclude that IMN, because of its philosophical flaws, proves to be an ill-advised strategy to counter the claims of IDC. Evolutionary scientists are on firmer ground if they discard supernatural explanations on purely evidential grounds, instead of ruling them out by philosophical fiat. (shrink)

The leading Intelligent Design theorist William Dembski (Rowman & Littlefield, Lanham MD, 2002) argued that the first No Free Lunch theorem, first formulated by Wolpert and Macready (IEEE Trans Evol Comput 1: 67–82, 1997), renders Darwinian evolution impossible. In response, Dembski’s critics pointed out that the theorem is irrelevant to biological evolution. Meester (Biol Phil 24: 461–472, 2009) agrees with this conclusion, but still thinks that the theorem does apply to simulations of evolutionary processes. According to Meester, the theorem shows (...) that simulations of Darwinian evolution, as these are typically set in advance by the programmer, are teleological and therefore non-Darwinian. Therefore, Meester argues, they are useless in showing how complex adaptations arise in the universe. Meester uses the term teleological inconsistently, however, and we argue that, no matter how we interpret the term, a Darwinian algorithm does not become non-Darwinian by simulation. We show that the NFL theorem is entirely irrelevant to this argument, and conclude that it does not pose a threat to the relevance of simulations of biological evolution. (shrink)

Although sciences are often conceptualized in terms of theory confirmation and hypothesis testing, an equally important dimension of scientific reasoning is the structure of problems that guide inquiry. This problem structure is evident in several concepts central to evolutionary developmental biology (Evo-devo)—constraints, modularity, evolvability, and novelty. Because problems play an important role in biological practice, they should be included in biological pedagogy, especially when treating the issue of scientific controversy. A key feature of resolving controversy is synthesizing methodologies from different (...) biological disciplines to generate empirically adequate explanations. Concentrating on problem structure illuminates this interdisciplinarity in a way that is often ignored when science is taught only from the perspective of theory or hypothesis. These philosophical considerations can assist life science educators in their continuing quest to teach biology to the next generation. -/- . (shrink)

A number of areas of biology raise questions about what is of value in the natural environment and how we ought to behave towards it: conservation biology, environmental science, and ecology, to name a few. Based on my experience teaching students from these and similar majors, I argue that the field of environmental ethics has much to teach these students. They come to me with pent-up questions and a feeling that more is needed to fully engage in their subjects, and (...) I believe some exposure to environmental ethics can help focus their interests and goals. I identify three primary areas in which environmental ethics can con- tribute to their education. The first is an examination of who (or what) should be considered to be part of our moral community (i.e., the community to whom we owe direct duties). Is it humans only? Or does it include all sentient life? Or all life? Or ecosystems considered holistically? Often, readings implicitly assume one or more of these answers; the goal is to make the student more sensitive to these implicit claims and to get them to think about the different reasons that support them. The second area, related to the first, is the application of the different answers concerning the extent of the ethical community to real environmental issues and problems. Students need to be aware of how the different answers concerning the moral community can imply conflicting answers for how we should act in certain cases and to think about ways to move toward conflict resolution. The third area in which environmental ethics can contribute is a more conceptual one, focusing on central concepts such as biodiversity, sustainability, species, and ecosystems. Exploring and evaluating various meanings of these terms will make students more reflective and thoughtful citizens and biologists, sensitive to the implications that different conceptual choices make. (shrink)