The official model of explanation proposed by the logical empiricists, the covering law model, is subject to familiar objections. The goal of the present paper is to explore an unofficial view of explanation which logical empiricists have sometimes suggested, the view of explanation as unification. I try to show that this view can be developed so as to provide insight into major episodes in the history of science, and that it can overcome some of the most serious difficulties besetting the (...) covering law model. (shrink)

Reductionism encompasses a set of ontological, epistemological, and methodological claims about the relation of different scientific domains. The basic question of reduction is whether the properties, concepts, explanations, or methods from one scientific domain (typically at higher levels of organization) can be deduced from or explained by the properties, concepts, explanations, or methods from another domain of science (typically one about lower levels of organization). Reduction is germane to a variety of issues in philosophy of science, including the structure of (...) scientific theories, the relations between different scientific disciplines, the nature of explanation, the diversity of methodology, and the very idea of theoretical progress, as well as to numerous topics in metaphysics and philosophy of mind, such as emergence, mereology, and supervenience. (shrink)

Methodological reductionists practice ‘wannabe reductionism’. They claim that one should pursue reductionism, but never propose how. I integrate two strains in prior work to do so. Three kinds of activities are pursued as “reductionist”. “Successional reduction” and inter-level mechanistic explanation are legitimate and powerful strategies. Eliminativism is generally ill-conceived. Specific problem-solving heuristics for constructing inter-level mechanistic explanations show why and when they can provide powerful and fruitful tools and insights, but sometimes lead to erroneous results. I show how traditional metaphysical (...) approaches fail to engage how science is done. The methods used do so, and support a pragmatic and non-eliminativist realism. (shrink)

As a working hypothesis for philosophy of science, the unity of science thesis has been decisively challenged in all its standard formulations; it cannot be assumed that the sciences presuppose an orderly world, that they are united by the goal of systematically describing and explaining this order, or that they rely on distinctively scientific methodologies which, properly applied, produce domain-specific results that converge on a single coherent and comprehensive system of knowledge. I first delineate the scope of arguments against global (...) unity theses. However implausible old-style global unity theses may now seem, I argue that unifying strategies of a more local and contingent nature do play an important role in scientific inquiry. This is particularly clear in archaeology where, to establish evidential claims of any kind, practitioners must exploit a range of inter-field and inter-theory connections. At the same time, the robustness of these evidential claims depends on significant disunity between the sciences from which archaeologists draw background assumptions and auxiliary hypotheses. This juxtaposition of unity with disunity poses a challenge to standard positions in the debate about scientific unity. (shrink)

This paper argues that conceptualizing unity as "interconnection" (rather than reduction) provides a more fruitful and versatile framework for the philosophical study of scientific unification. Building on the work of Darden and Maull, Kitcher, and Kincaid, I treat unity as a relationship between fields: two fields become more integrated as the number and/or significance of interfield connections grow. Even when reduction fails, two theories or fields can be unified (integrated) in significant ways. I highlight two largely independent dimensions of unification. (...) Fields are theoretically unified to the extent that we understand how the ontologies, concepts, and generalizations of these fields are connected. (Reductionism is one form of theoretical unity, but not the only form). Fields are practically unified through heuristic connections (e.g., using the heuristics of one field to generate hypotheses in another field) and by the development of methods for integrating the qualitatively distinct bodies of data generated by the two fields. I discuss the relationship between paleontological and neontological systematics to illustrate the utility of conceptualizing unity as interconnection. (shrink)

In this paper I respond to Wim van der Steen''s arguments against the supposed current overemphasis on norms ofcoherence andinterdisciplinary integration in biology. On the normative level, I argue that these aremiddle-range norms which, although they may be misapplied in short-term attempts to solve (temporarily?) intractable problems, play a guiding role in the longer-term treatment of biological problems. This stance is supported by a case study of apartial success story, the development of the one gene — one enzyme hypothesis. As (...) that case shows, thegoal of coherent interdisciplinary integration not only provides guidance for research, but also provides the standard for recognizingfailed integrations of the sort that van der Steen criticizes. (shrink)

The Tree of Life hypothesis frames the evolutionary process as a series of events whereby lineages diverge from one another, thus creating the diversity of life as descendent lineages modify properties from their ancestors. This hypothesis is under scrutiny due to the strong evidence for lateral gene transfer between distantly related bacterial taxa, thereby providing extant taxa with more than one parent. As a result, one argues, the Tree of Life becomes confounded as the original branching structure is gradually superseded (...) by reticulation, ultimately losing its ability to serve as a model for bacterial evolution. Here we address a more fundamental issue: is there a Tree of Life that results from bacterial evolution without considering such lateral gene transfers? Unlike eukaryotic speciation events, lineage separation in bacteria is a gradual process that occurs over tens of millions of years, whereby genetic isolation is established on a gene-by-gene basis. As a result, groups of closely related bacteria, while showing robust genetic isolation as extant lineages, were not created by an unambiguous series of lineage-splitting events. Rather, a temporal fragmentation of the speciation process results in cognate genes showing different genetic relationships. We argue that lineage divergence in bacteria does not produce a tree-like framework, and inferences drawn from such a framework have the potential to be incorrect and misleading. Therefore, the Tree of Life is an inappropriate paradigm for bacterial evolution regardless of the extent of gene transfer between distantly related taxa. (shrink)

Recently improved understanding of evolutionary processes suggests that tree-based phylogenetic analyses of evolutionary change cannot adequately explain the divergent evolutionary histories of a great many genes and gene complexes. In particular, genetic diversity in the genomes of prokaryotes, phages, and plasmids cannot be fit into classic tree-like models of evolution. These findings entail the need for fundamental reform of our understanding of molecular evolution and the need to devise alternative apparatus for integrated analysis of these genomes. We advocate the development (...) of integrative phylogenomics for analyzing these genomes and their histories, with tools suited to analyzing the importance of lateral gene transfer (LGT) and of DNA evolution in extra-cellular mobile genetic elements (e.g., viruses, plasmids). These phenomena greatly increase the complexity of relationships among interacting genetic partners, as they exchange functional genetic units. We examine the ontology of functional genetic units, interacting genetic partners, and emergent genetic associations, argue that these three categories of entities are required for a successful integrated phylogenomics. We conclude with arguments to suggest that the proposed new perspective and associated tools are suitable, and perhaps required, as a replacement for the bifurcating trees that have dominated evolutionary thinking for the last 150 years. (shrink)

Mutation and lateral transfer are two categories of processes generating genetic diversity in prokaryotic genomes. Their relative importance varies between lineages, yet both are complementary rather than independent, separable evolutionary forces. The replication process inevitably merges together their effects on the genome. We develop the concept of “open lineages” to characterize evolutionary lineages that over time accumulate more changes in their genomes by lateral transfer than by mutation. They contrast with “closed lineages,” in which most of the changes are caused (...) by mutation. Open and closed lineages are interspersed along the branches of any tree of prokaryotes. This patchy distribution conflicts with the basic assumptions of traditional phylogenetic approaches. As a result, a tree representation including both open and closed lineages is a misrepresentation. The evolution of all prokaryotic lineages cannot be studied under a single model unless new phylogenetic approaches that are more pluralistic about lineage evolution are designed. (shrink)

Ernst Mayr’s influence on philosophy of biology has given the field a particular perspective on evolution, phylogeny and life in general. Using debates about the tree of life as a guide, I show how Mayrian evolutionary biology excludes numerous forms of life and many important evolutionary processes. Hybridization and lateral gene transfer are two of these processes, and they occur frequently, with important outcomes in all domains of life. Eukaryotes appear to have a more tree-like history because successful lateral events (...) tend to occur among more closely related species, or at a lower frequency, than in prokaryotes, but this is a difference of degree rather than kind. Although the tree of life is especially problematic as a representation of the evolutionary history of prokaryotes, it can function more generally as an illustration of the limitations of a standard evolutionary perspective. Moreover, for philosophers, questions about the tree of life can be applied to the Mayrian inheritance in philosophy of biology. These questions make clear that the dichotomy of life Mayr suggested is based on too narrow a perspective. An alternative to this dichotomy is a multidimensional continuum in which different strategies of genetic exchange bestow greater adaptiveness and evolvability on prokaryotes and eukaryotes. (shrink)

This paper examines the nature of theory structure in biology and considers the implications of those theoretical structures for theory reduction. An account of biological theories as interlevel prototypes embodying causal sequences, and related to each other by strong analogies, is presented, and examples from the neurosciences are provided to illustrate these middle-range theories. I then go on to discuss several modifications of Nagel''s classical model of theory reduction, and indicate at what stages in the development of reductions these models (...) might best apply. Finally I consider several implications of these analyses of theory structure and reduction for disciplinary integration in biology. (shrink)

Frequent lateral genetic transfer undermines the existence of a unique “tree of life” that relates all organisms. Vertical inheritance is nonetheless of vital interest in the study of microbial evolution, and knowing the “tree of cells” can yield insights into ecological continuity, the rates of change of different cellular characters, and the evolutionary plasticity of genomes. Notwithstanding within-species recombination, the relationships most frequently recovered from genomic data at shallow to moderate taxonomic depths are likely to reflect cellular inheritance. At the (...) same time, it is clear that several types of ‘average signals’ from whole genomes can be highly misleading, and the existence of a central tendency must not be taken as prima facie evidence of vertical descent. Phylogenetic networks offer an attractive solution, since they can be formulated in ways that mitigate the misleading aspects of hybrid evolutionary signals in genomes. But the connections in a network typically show genetic relatedness without distinguishing between vertical and lateral inheritance of genetic material. The solution may lie in a compromise between strict tree-thinking and network paradigms: build a phylogenetic network, but identify the set of connections in the network that are potentially due to vertical descent. Even if a single tree cannot be unambiguously identified, choosing a subnetwork of putative vertical connections can still lead to drastic reductions in the set of candidate vertical hypotheses. (shrink)

A recent study(1) of sequence data from many different proteins has suggested that contemporary prokaryotes and eukaryotes may have shared a common ancestor as recently as 2 billion years ago (the molecular clock). Strong evidence from the geological record, however, indicates that oxygen‐producing microorganisms, perhaps similar to modern cyanobacteria, existed 3.5 billion years ago. The fossil evidence, therefore, suggests that any common ancestor of prokaryotes and eukaryotes must have existed at least 1.5 billion years earlier than suggested by the molecular (...) clock evidence. The discrepancy between molecular and geological evidence for the age of modern cells is considered here, as are aspects of gene descent in the tree of life that might help to account for it. (shrink)

Metazoa are one of the great monophyletic groups of organisms. They comprise several major groups of organisms readily recognizable based on their anatomy. These major groups include the Bilateria (animals with bilateral symmetry), Cnidaria (jellyfish, corals and other closely related animals), Porifera (sponges), Ctenophores (comb jellies) and a phylum currently made up of a single species, the Placozoa. Attempts to systematize the relationships of these major groups as well as to determine relationships within the groups have been made for nearly (...) two centuries. Many of the attempts have led to frustration, because of a lack of resolution between and within groups. Other attempts have led to “a new animal phylogeny”. Now, a study by Dunn et al.,1 using the expresssed sequence tag (EST) approach to obtaining high‐throughput large phylogenetic matrices, presents an “even newer” animal phylogeny. There are two major aspects of this study that should be of interest to the general biological community. First, the methods used by the authors to generate their phylogenetic hypotheses call for close examination. Second, the relationships of animal taxa in their resultant trees also prompt further discussion. BioEssays 30:1043–1047, 2008. © 2008 Wiley Periodicals, Inc. (shrink)

Many studies of the unification of science focus on the theories of different disciplines. The model for integration is the theory reduction model. This paper argues that the embodiment of theories in scientists, and the institutions in which scientists work and the instruments they employ, are critical to the sort of integration that actually occurs in science. This paper examines the integration of scientific endeavors that emerged in cell biology in the period after World War II when the development of (...) cell fractionation and electron microscopy made serious investigations of cell organelles possible. One surprising feature of such integration is that it generated further disintegration as the new institutions of cell biology separated the practitioners of the new discipline from other, closely related biological disciplines. (shrink)

Why has it been so difficult to integrate paleontology and mainstream evolutionary biology? Two common answers are: (1) the two fields have fundamentally different aims, and (2) the tensions arise out of disciplinary squabbles for funding and prestige. This paper examines the role of fossil data in phylogeny reconstruction in order to assess these two explanations. I argue that while cladistics has provided a framework within which to integrate fossil character data, the stratigraphic (temporal) component of fossil data has been (...) harder to integrate. A close examination of how fossil data have been used in phylogeny reconstruction suggests that neither explanation is adequate. While some of the tensions between the fields may be intellectual turf wars, the second explanation downplays the genuine difficulty of combining the distinctive data of the two fields. Furthermore, it is simply not the case that the two fields pursue completely distinct aims. Systematists do disagree about precisely how to represent phylogeny (e.g., minimalist cladograms or trees with varying levels of detail) but given that every tree presupposes a pattern of branching (a cladogram), these aims are not completely distinct. The central problem has been developing methods that allow scientists to incorporate the distinctive bodies of data generated by these two fields. Further case studies will be required to determine if this explanation holds for other areas of interaction between paleontology and neontology. (shrink)