Several authors have argued that causes differ in the degree to which they are ‘specific’ to their effects. Woodward has used this idea to enrich his influential interventionist theory of causal explanation. Here we propose a way to measure causal specificity using tools from information theory. We show that the specificity of a causal variable is not well-defined without a probability distribution over the states of that variable. We demonstrate the tractability and interest of our proposed measure by measuring the (...) specificity of coding DNA and other factors in a simple model of the production of mRNA. (shrink)

Philosophers and historians of biology have argued that genes are conceptualized differently in different fields of biology and that these differences influence both the conduct of research and the interpretation of research by audiences outside the field in which the research was conducted. In this paper we report the results of a questionnaire study of how genes are conceptualized by biological scientists at the University of Sydney, Australia. The results provide tentative support for some hypotheses about conceptual differences between different (...) fields of biological research. (shrink)

Kenneth C. Schaffner's paper is an important contribution to the literature on behavioral genetics and on genetics in general. Schaffner has a long record of injecting real molecular biology into philosophical discussions of genetics. His treatments of the reduction of Mendelian to molecular genetics first drew philosophical attention to the problems of detail that have fuelled both anti-reductionism and more sophisticated models of theory reduction. An injection of molecular detail into discussions of genetics is particularly necessary at the present time, (...) when so many philosophers seem happy to discuss the philosophical and ethical implications of molecular biology using gene concepts derived from evolutionary biology ). Schaffner has long advocated the view that the philosophy of biology should be more than the philosophy of evolution. This paper shows how radically a picture of gene action derived from molecular biology undercuts the popular picture associated with a more evolutionary view of genes as units of heredity or as ‘difference-makers’ mediated by the ‘black box’ of development. (shrink)

Philosophers and historians of biology have argued that genes are conceptualized differently in different fields of biology and that these differences influence both the conduct of research and the interpretation of research by audiences outside the field in which the research was conducted. In this paper we report the results of a questionnaire study of how genes are conceptualized by biological scientists at the University of Sydney, Australia. The results provide tentative support for some hypotheses about conceptual differences between different (...) fields of biological research. (shrink)

Multilevel research strategies characterize contemporary molecular inquiry into biological systems. We outline conceptual, methodological, and explanatory dimensions of these multilevel strategies in microbial ecology, systems biology, protein research, and developmental biology. This review of emerging lines of inquiry in these fields suggests that multilevel research in molecular life sciences has significant implications for philosophical understandings of explanation, modeling, and representation.

This book is intended to be a standard reference work on the frontal lobes for researchers, clinicians, and students in the fields of neurology, neuroscience, ...

Microbial ecology is flourishing, and in the process, is making contributions to how the ecology and biology of large organisms is understood. Ongoing advances in sequencing technology and computational methods have enabled the collection and analysis of vast amounts of molecular data from diverse biological communities. While early studies focused on cataloguing microbial biodiversity in environments ranging from simple marine ecosystems to complex soil ecologies, more recent research is concerned with community functions and their dynamics over time. Models and concepts (...) from traditional ecology have been used to generate new insight into microbial communities, and novel system-level models developed to explain and predict microbial interactions. The process of moving from molecular inventories to functional understanding is complex and challenging, and never more so than when many thousands of dynamic interactions are the phenomena of interest. We outline the process of how epistemic transitions are made from producing catalogues of molecules to achieving functional and predictive insight, and show how those insights not only revolutionize what is known about biological systems but also about how to do biology itself. Examples will be drawn primarily from analyses of different human microbiota, which are the microbial consortia found in and on areas of the human body, and their associated microbiomes (the genes of those communities). Molecular knowledge of these microbiomes is transforming microbiological knowledge, as well as broader aspects of human biology, health and disease. (shrink)

The presence and role of microbes in human cancers has come full circle in the last century. Tumors are no longer considered aseptic, but implications for cancer biology and oncology remain underappreciated. Opportunities to identify and build translational diagnostics, prognostics, and therapeutics that exploit cancer's second genome—the metagenome—are manifold, but require careful consideration of microbial experimental idiosyncrasies that are distinct from host-centric methods. Furthermore, the discoveries of intracellular and intra-metastatic cancer bacteria necessitate fundamental changes in describing clonal evolution and selection, (...) reflecting bidirectional interactions with non-human residents. Reconsidering cancer clonality as a multispecies process similarly holds key implications for understanding metastasis and prognosing therapeutic resistance while providing rational guidance for the next generation of bacterial cancer therapies. Guided by these new findings and challenges, this Review describes opportunities to exploit cancer's metagenome in oncology and proposes an evolutionary framework as a first step towards modeling multispecies cancer clonality. Also see the video abstract here: https://youtu.be/-WDtIRJYZSs. (shrink)

Attention research with prefrontal patients supports Merker's argument regarding the crucial role for the midbrain in higher cognition, through largely overlooked and misunderstood prefrontotectal connectivity. However, information theoretic analyses reveal that both exogenous (i.e., collicular) and endogenous (prefrontal) sources of information are responsible for large-scale context-sensitive brain dynamics, with prefrontal cortex being at the top of the hierarchy for cognitive control. (Published Online May 1 2007).

Aggleton & Brown argue that a hippocampal-anterior thalamic system supports the “recollection” of contextual information about previous events, and that a separate perirhinal-medial dorsal thalamic system supports detection of stimulus “familiarity.” Although there is a growing body of human literature that is in agreement with these claims, when recollection and familiarity have been examined in amnesics using the process dissociation or the remember/know procedures, the results do not seem to provide consistent support. We reexamine these studies and describe the results (...) of an additional experiment using a receiver operating characteristic (ROC) technique. The results of the reanalysis and the ROC experiment are consistent with Aggleton & Brown's proposal. Patients with damage to both regions exhibit severe deficits in recollection and smaller, but consistent, deficits in familiarity. (shrink)