Online research in philosophy

Kincaid argues that molecular biology provides little support for the reductionist program, that biochemistry does not reveal common mechanisms, indeed that biochemical theory obstructs discovery. These assertions clash with biologists' stated advocacy of reductionist programs and their claims about the consequent unity of experimental biology. This striking disagreement goes beyond differences in meaning granted to the terms. More significant is Kincaid's misunderstanding of what biochemists do, for a closer look at scientific practice-- and one of Kincaid's examples--reveals substantial progress toward explaining biological function with biochemical models. With the molecular detail emerge unifying generalizations as well as further aspects of the functional processes.

This book provides a comprehensive guide to the conceptual methodological, and epistemological problems of biology, and treats in depth the major developments in molecular biology and evolutionary theory that have transformed both biology and its philosophy in recent decades. At the same time the work is a sustained argument for a particular philosophy of biology that unifies disparate issues and offers a framework for expectations about the future directions of the life sciences. The argument explores differences between autonomist and anti-autonomist views of biology. The result is a vindication of reductionism, but one that is unexpectedly hollow. For it leaves the exponents of the autonomy of biology from physical science with as much as their view of biology really requires - and rather more than the reductionist might comfortably concede. Professor Rosenberg shows how the problems of the philosophy of biology are interconnected and how their solutions are interdependent, However, this book focuses more on the direct concerns of biologists, rather than the traditional agenda of philosophers' problems about biology. This departure from earlier books on the subject results both in greater understanding and relevance of the philosophy of science to biology as a whole.

The applicability of Nagel's concept of theory reduction, and related concepts of reduction, to the reduction of genetics to molecular biology is examined using the lactose operon in Escherichia coli as an example. Geneticists have produced the complete nucleotide sequence of two of the genes which compose this operon. If any example of reduction in genetics should fit Nagel's analysis, the lactose operon should. Nevertheless, Nagel's formal conditions of theory reduction are inapplicable in this case. Instead, it is argued that genetics has been partially reduced to molecular biology in the sense of token-token reduction.

Biologists and historians often present natural history and molecular biology as distinct, perhaps conflicting, fields in biological research. Such accounts, although supported by abundant evidence, overlook important areas of overlap between these areas. Focusing upon examples drawn particularly from systematics and molecular evolution, I argue that naturalists and molecular biologists often share questions, methods, and forms of explanation. Acknowledging these interdisciplinary efforts provides a more balanced account of the development of biology during the post-World War II era.

The comprehension of living organisms in all their complexity poses a major challenge to the biological sciences. Recently, systems biology has been proposed as a new candidate in the development of such a comprehension. The main objective of this paper is to address what systems biology is and how it is practised. To this end, the basic tools of a systems biological approach are explored and illustrated. In addition, it is questioned whether systems biology ‘revolutionizes’ molecular biology and ‘transcends’ its assumed reductionism. The strength of this claim appears to depend on how molecular and systems biology are characterised and on how reductionism is interpreted. Doing credit to molecular biology and to methodological reductionism, it is argued that the distinction between molecular and systems biology is gradual rather than sharp. As such, the classical challenge in biology to manage, interpret and integrate biological data into functional wholes is further intensified by systems biology’s use of modelling and bioinformatics, and by its scale enlargement.

The theory of concepts advanced in the dissertation aims at accounting for a) how a concept makes successful practice possible, and b) how a scientific concept can be subject to rational change in the course of history. Traditional accounts in the philosophy of science have usually studied concepts in terms only of their reference; their concern is to establish a stability of reference in order to address the incommensurability problem. My discussion, in contrast, suggests that each scientific concept consists of three components of content: 1) reference, 2) inferential role, and 3) the epistemic goal pursued with the concept's use. I argue that in the course of history a concept can change in any of these three components, and that change in one component—including change of reference—can be accounted for as being rational relative to other components, in particular a concept's epistemic goal.

The belief in the Darwinian theory of evolution appeared to be shaken when one tried to interpret statements of molecular biology in it. As a consequence there arose a theory of non-Darwinian neutral evolution. The supporters of this theory believe that under natural conditions no factors exist which can distinguish and select organisms on their internal (molecular) structure. In the opinion of these neutralists natural selection cannot in principle control the molecular constitution of organisms. Contrary to the viewpoint of the critics of neutralism it is impossible to admit that nucleic acids, proteins and other biomolecules can evolve without the participation of natural selection. This controversy in contemporary theoretical biology can be solved by integrating the conceptions of molecular ecology with Darwinian theory. Molecular ecology acknowledges the interactions of organisms by means of chemical substances synthesized by them. Such chemical ecological factors play a leading part in the selective stages of biomolecular evolution. These diverse chemical ecological interrelations take place intensively when living beings interact with parasitic microbes.

After the discovery of the structure of DNA in 1953, scientists working in molecular biology embraced reductionism—the theory that all complex systems can be understood in terms of their components. Reductionism, however, has been widely resisted by both nonmolecular biologists and scientists working outside the field of biology. Many of these antireductionists, nevertheless, embrace the notion of physicalism—the idea that all biological processes are physical in nature. How, Alexander Rosenberg asks, can these self-proclaimed physicalists also be antireductionists? With clarity and wit, Darwinian Reductionism navigates this difficult and seemingly intractable dualism with convincing analysis and timely evidence. In the spirit of the few distinguished biologists who accept reductionism—E. O. Wilson, Francis Crick, Jacques Monod, James Watson, and Richard Dawkins—Rosenberg provides a philosophically sophisticated defense of reductionism and applies it to molecular developmental biology and the theory of natural selection, ultimately proving that the physicalist must also be a reductionist.

Two decades of critique have sensitized historians and philosophers of science to the inadequacies of conventional dichotomies between theory and practice, thereby prompting the search for new ways of writing about science that are less beholden than the old ways to the epistemological mores of theoretical physics, and more faithful to the actual practices not only of physics but of all the natural sciences. The need for alternative descriptions seems particularly urgent if one is to understand the place of theory (and, in parallel, the role of modeling) in contemporary molecular biology, a science where, until now, no division between theory and experiment has obtained, and where distinctions between representing and intervening, and more generally, between basic and applied science, are daily becoming more blurred. Indeed, the very division between theory and experiment threatens to slight the extensive and sophisticated theoretical analyses (and even modeling) on which experimental work in contemporary molecular biology so often depends. My aim in this paper is to find a way of talking about theoretical practices in biology that is directly rooted in the mix of conceptual and material work that biologists do. As an example of such theoretical practices, I choose for the focus of my analysis the development of a model for gene regulation out of the experimental work of Eric Davidson and his colleagues at Cal Tech.

The theory of concepts advanced in the dissertation aims at accounting for a) how a concept makes successful practice possible, and b) how a scientific concept can be subject to rational change in the course of history. Traditional accounts in the philosophy of science have usually studied concepts in terms only of their reference; their concern is to establish a stability of reference in order to address the incommensurability problem. My discussion, in contrast, suggests that each scientific concept consists of three components of content: 1) reference, 2) inferential role, and 3) the epistemic goal pursued with the concept's use. I argue that in the course of history a concept can change in any of these three components, and that change in one component—including change of reference—can be accounted for as being rational relative to other components, in particular a concept's epistemic goal. This semantic framework is applied to two cases from the history of biology: the homology concept as used in 19th and 20th century biology, and the gene concept as used in different parts of the 20th century. The homology case study argues that the advent of Darwinian evolutionary theory, despite introducing a new definition of homology, did not bring about a new homology concept (distinct from the pre-Darwinian concept) in the 19th century. Nowadays, however, distinct homology concepts are used in systematics/evolutionary biology, in evolutionary developmental biology, and in molecular biology. The emergence of these different homology concepts is explained as occurring in a rational fashion. The gene case study argues that conceptual progress occurred with the transition from the classical to the molecular gene concept, despite a change in reference. In the last two decades, change occurred internal to the molecular gene concept, so that nowadays this concept's usage and reference varies from context to context. I argue that this situation emerged rationally and that the current variation in usage and reference is conducive to biological practice. The dissertation uses ideas and methodological tools from the philosophy of mind and language, the philosophy of science, the history of science, and the psychology of concepts.