Online research in philosophy

Both von Neumann and Wiener were outsiders to biology. Both were inspired by biology and both proposed models and generalizations that proved inspirational for biologists. Around the same time in the 1940s von Neumann developed the notion of self reproducing automata and Wiener suggested an explication of teleology using the notion of negative feedback. These efforts were similar in spirit. Both von Neumann and Wiener used mathematical ideas to attack foundational issues in biology, and the concepts they articulated had lasting (...) effect. But there were significant differences as well. Von Neumann presented a how-possibly model, which sparked interest by mathematicians and computer scientists, while Wiener collaborated more directly with biologists, and his proposal influenced the philosophy of biology. The two cases illustrate different strategies by which mathematicians, the “professional outsiders” of science, can choose to guide their engagement with biological questions and with the biological community, and illustrate different kinds of generalizations that mathematization can contribute to biology. The different strategies employed by von Neumann and Wiener and the types of models they constructed may have affected the fate of von Neumann’s and Wiener’s ideas – as well as the reputation, in biology, of von Neumann and Wiener themselves. (shrink)

Organisms inherit various kinds of developmental information and cues from their parents. The study of inheritance systems is aimed at identifying and classifying the various mechanisms and processes of heredity, the types of hereditary information that is passed on by each, the functional interaction between the different systems, and the evolutionary consequences of these properties. We present the discussion of inheritance systems in the context of several debates. First, between proponents of monism about heredity (gene-centric views), holism about heredity (Developmental (...) Systems Theory), and those stressing the role of multiple systems of inheritance. Second, between those analyzing inheritance solely in terms of replication and transmission, and views that stress the multi-generation reproduction of phenotypic traits. A third debate is concerned with different criteria that have been proposed for identifying and delimiting inheritance systems. A fourth controversy revolves around the significance of the “Lamarckian” aspects of some of the inheritance systems that have been identified, such as epigenetic inheritance and behavioral inheritance, that allow the transmission of environmentally induced characters (i.e., “soft inheritance”). (shrink)

This article is arranged around two general claims and a thought experiment. I begin by suggesting that the genome should be studied as a developmental system, and that genes supervene on genomes (rather than the other way around). I move on to present a thought experiment that illustrates the implications a dynamic view of the genome has for central concepts in biology, in particular the information content of the genome, and the notion of responses to stress.

Recent and not so recent advances in our molecular understanding of the genome make the once prevalent view of the genome as a passive container of genetic information (i.e., genes) untenable, and emphasize the importance of the internal organization and re-organization dynamics of the genome for both development and evolution. While this conclusion is by now well accepted, the construction of a comprehensive conceptual framework for studying the genome as a dynamic system, capable of self-organization and adaptive behavior is still (...) underway. This work deals with the effect of such a conceptual shift on evolutionary thought. Specifically, I try to articulate the conceptual commitments and obligations of views that privilege explanatorily or causally the genome, its dynamics and mechanisms, over genes. I refer to this class of views as belonging to ‘the genome perspective’. (shrink)

The review focuses on Huxley’s debt to Richard Goldschmidt and Cyril Darlington. I discuss the conceptions of the genome developed by Goldschmidt and Darlington and their continuing relevance.

Many natural and biological phenomena can be depicted as networks. Theoretical and empirical analyses of networks have become prevalent. I discuss theoretical biases involved in the delineation of biological networks. The network perspective is shown to dissolve the distinction between regulatory architecture and regulatory state, consistent with the theoretical impossibility of distinguishing a priori between “program” and “data”. The evolutionary significance of the dynamics of trans-generational and inter-organism regulatory networks is explored and implications are presented for understanding the evolution of (...) the biological categories development-heredity; plasticity-evolvability; and epigenetic-genetic. (shrink)

This volume joins a growing list of books, monographs, and proceedings from scientific meetings that attempt to consolidate the wide spectrum of approaches emphasizing the role of development in evolution into a coherent and productive synthesis, often called evo-devo. Evo-devo is seen as a replacement or amendment of the modern synthesis that has dominated the field of evolution since the 1940s and which, as even its architects confessed, was fundamentally incomplete because development remained outside its theoretical framework (Mayr and Provine (...) 1980).As the volume attests, there is now a strong feeling that the time is ripe for the onsolidation of evo-devo, and that the field is mature enough so that mapping the theoretical terrain and experimental approaches is both feasible and scientifically productive. Now is an appropriate time to try to weave the strands of reasoning leading to the developmental perspective and offer a synthesis. (shrink)

Richard Goldschmidt famously rejected the notion of atomic and corpuscular genes, arranged on the chromosome like beads-on-a-string. I provide an exegesis of Goldschmidt’s intuition by analyzing his repeated and extensive use of metaphorical language and analogies in his attempts to convey his notion of the nature of the genetic material and specifically the significance of chromosomal pattern. The paper concentrates on Goldschmidt’s use of metaphors in publications spanning 1940-1955. -/- .

The dichotomy between Nature and Nurture, which has been dismantled within the framework of development, remains embodied in the notions of plasticity and evolvability. We argue that plasticity and evolvability, like development and heredity, are neither dichotomous nor distinct: the very same mechanisms may be involved in both, and the research perspective chosen depends to a large extent on the type of problem being explored and the kinds of questions being asked. Epigenetic inheritance leads to transgenerationally extended plasticity, and developmentally-induced (...) heritable epigenetic variations provide additional foci for selection that can lead to evolutionary change. Moreover, hereditary innovations may result from developmentally induced large-scale genomic repatterning events, which are akin to Goldschmidtian “systemic mutations”. The epigenetic mechanisms involved in repatterning can be activated by both environmental and genomic stress, and lead to phylogenetic as well as ontogenetic changes. Hence, the effects and the mechanisms of plasticity directly contribute to evolvability. (shrink)