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)
This chapter offers a review of standard views about the requirements for natural selection to shape evolution and for the sorts of ‘units’ on which selection might operate. It then summarizes traditional arguments for genic selectionism, i.e., the view that selection operates primarily on genes (e.g., those of G. C. Williams, Richard Dawkins, and David Hull) and traditional counterarguments (e.g., those of William Wimsatt, Richard Lewontin, and Elliott Sober, and a diffuse group based on life history strategies). It then offers (...) a series of responses to the arguments, based on more contemporary considerations from molecular genetics, offered by Carmen Sapienza. A key issue raised by Sapienza concerns the degree to which a small number of genes might be able to control much of the variation relevant to selection operating on such selectively critical organs as hearts. The response to these arguments suggests that selection acts on many levels at once and that sporadic selection, acting with strong effects, can act successively on different key traits (and genes) while maintaining a balance among many potentially conflicting demands faced by organisms within an evolving lineage. (shrink)
This paper is devoted to an examination of the discovery, characterization, and analysis of the functions of microRNAs, which also serves as a vehicle for demonstrating the importance of exploratory experimentation in current (post-genomic) molecular biology. The material on microRNAs is important in its own right: it provides important insight into the extreme complexity of regulatory networks involving components made of DNA, RNA, and protein. These networks play a central role in regulating development of multicellular organisms and illustrate the importance (...) of epigenetic as well as genetic systems in evolution and development. The examination of these matters yields principled arguments for the historicity of the functions of key biological molecules and for the indispensability of exploratory experimentation in contemporary molecular biology as well as some insight into the complex interplay between exploratory experimentation and hypothesis-driven science. This latter result is not only of importance for philosophy of science, but also of practical importance for the evaluation of grant proposals, although the elaboration of this latter claim must be left for another occasion. (shrink)
The essays in this collection examine developments in three fundamental biological disciplines--embryology, evolutionary biology, and genetics--in conflict with each other for much of the twentieth century. They consider key methodological problems and the difficulty of overcoming them. Richard Burian interweaves historical appreciation of the settings within which scientists work, substantial knowledge of the biological problems at stake and the methodological and philosophical issues faced in integrating biological knowledge drawn from disparate sources.
: Philosophers of science turned to historical case studies in part in response to Thomas Kuhn's insistence that such studies can transform the philosophy of science. In this issue Joseph Pitt argues that the power of case studies to instruct us about scientific methodology and epistemology depends on prior philosophical commitments, without which case studies are not philosophically useful. Here I reply to Pitt, demonstrating that case studies, properly deployed, illustrate styles of scientific work and modes of argumentation that are (...) not well handled by currently standard philosophical analyses. I illustrate these claims with exemplary findings from case studies dealing with exploratory experimentation and with interdisciplinary cooperation across sciences to yield multiple independent means of access to theoretical entities. The latter cases provide examples of ways that scientists support claims about theoretical entities that are not available in work performed within a single discipline. They also illustrate means of correcting systematic biases that stem from the commitments of each discipline taken separately. These findings illustrate the transformative power of case study methods, allow us to escape from the horns of Pitt's "dilemma of case studies," and vindicate some of the post-Kuhn uses to which case studies have been put. (shrink)
Biology deals, notoriously, with complex systems. In discussing biological methodology, all three papers in this symposium honor the complexity of biological subject matter by preferring models and theories built to reflect the details of complex systems to models based on broad general principles or laws. Rheinberger's paper, the most programmatic of the three, provides a framework for the epistemology of discovery in complex systems. A fundamental problem is raised for Rheinberger's epistemology, namely, how to understand the referential continuity of the (...) theoretical terms and concepts employed in typical case studies involving complex systems. (shrink)
Sober (1992) has recently evaluated Brandon's (1982, 1990; see also 1985, 1988) use of Salmon's (1971) concept of screening-off in the philosophy of biology. He critiques three particular issues, each of which will be considered in this discussion.
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)
We offer a systematic examination of propensity interpretations of fitness, which emphasizes the role that fitness plays in evolutionary theory and takes seriously the probabilistic character of evolutionary change. We distinguish questions of the probabilistic character of fitness from the particular interpretations of probability which could be incorporated. The roles of selection and drift in evolutionary models support the view that fitness must be understood within a probabilistic framework, and the specific character of organism/environment interactions supports the conclusion that fitness (...) must be understood as a propensity rather than as a limiting frequency. (shrink)
These comments center on the methodological stance that Howard and Maiocchi recommend to us when we are doing history of philosophy. If Howard and Maiocchi are right, both Duhem and Einstein developed closely related versions of conventionalism and realism, and in both of their philosophies the conventionalist and realist moments were mutually compatible. Duhem's holism and, arguably, Einstein's as well, denies the need for across-the-board literalism, and both of them had important reasons for denying that convergence was required or even (...) desirable for realism. Thus, for those who are caught up in the current disputes, serious consideration of the discrepancies between the standard current versions of realism and conventionalism and the positions that contextualist analyses reveal to have been advocated by Duhem and Einstein may uncover some of the tacit assumptions that impede the resolution or advancement of our disputes. (shrink)
The formal framework of Kauffman (1991) depicts the constraints of self-organization on the evolution of complex systems and the relation of self-organization to selection. We discuss his treatment of 'generic constraints' as sources of order (section 2) and the relation between adaptation and organization (section 3). We then raise a number of issues, including the role of adaptation in explaining order (section 4) and the limitations of formal approaches in explaining the distinctively biological (section 5). The principal question we pose (...) is the relation of generic constraints on evolution to more specific local constraints, imposed, for example, by the characteristic materials out of which organisms are constructed, the accidental features characteristic of the Bauplan of a lineage, and the local vicissitudes of adaptation. We offer no answer to this large question. (shrink)
In this study we have examined the reception of Mendelism in France from 1900 to 1940, and the place of some of the extra-Mendelian traditions of research that contributed to the development of genetics in France after World War II.
History of science, it has been argued, has benefited philosophers of science primarily by forcing them into greater contact with "real science." In this paper I argue that additional major benefits arise from the importance of specifically historical considerations within philosophy of science. Loci for specifically historical investigations include: (1) making and evaluating rational reconstructions of particular theories and explanations, (2) estimating the degree of support earned by particular theories and theoretical claims, and (3) evaluating proposed philosophical norms for the (...) evaluation of the degree of support for theories and the worth of explanations. More generally, I argue that theories develop and change structure with time, that (like biological species) they are historical entities. Accordingly, both the identification and the evaluation of theories are essentially historical in character. (shrink)