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)

First Published in 1999. Routledge is an imprint of Taylor & Francis, an informa company.

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.

The unexpected roles of the microbiota in cancer challenge explanations of carcinogenesis that focus on tumor-intrinsic properties. Most tumors contain bacteria and viruses, and the host’s proximal and distal microbiota influence both cancer incidence and therapeutic responsiveness. Continuing the history of cancer–microbe research, these findings raise a key question: to what extent is the microbiota relevant for clinical oncology? We approach this by critically evaluating three issues: how the microbiota provides a predictive biomarker of cancer growth and therapeutic responsiveness, the (...) microbiota’s causal role(s) in cancer development, and how therapeutic manipulations of the microbiota improve patient outcomes in cancer. Clarifying the conceptual and empirical aspects of the cancer-associated microbiota can orient future research and guide its implementation in clinical oncology. (shrink)

In vertebrates it is often found that if one considers a group of genes clustered on a certain chromosome, then the homologues of those genes often form another cluster on a different chromosome. There are four explanations, not necessarily mutually exclusive, to explain how such homologous clusters appeared. Homologous clusters are expected at a low probability even if genes are distributed at random. The duplication of a subset of the genome might create homologous clusters, as would a duplication of the (...) entire genome. Alternatively, it may be adaptive for certain combinations of genes to cluster, although clearly the genes must have duplicated prior to rearrangement into clusters. Molecular phylogenetics provides a means to examine the origins of homologous clusters, although it is difficult to discriminate between the different explanations using current data. However, with more extensive sequencing and mapping of vertebrate genomes, especially those of the early diverging chordates, it should soon become possible to resolve the origins of homologous clusters. BioEssays 21:697–703, 1999. © 1999 John Wiley & Sons, Inc. (shrink)

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)

Large‐scale characterization of the human microbiota has largely focused on Western adults, yet these populations may be uncharacteristic because of their diets and lifestyles. In particular, the rise of “Western diseases” may in part stem from reduced exposure to, or even loss of, microbes with which humans have coevolved. Here, we review beneficial microbes associated with pathogen resistance, highlighting the emerging role of complex microbial communities in protecting against disease. We discuss ways in which modern lifestyles and practices may deplete (...) physiologically important microbiota, and explore prospects for reintroducing or encouraging the growth of beneficial microbes to promote the restoration of healthy microbial ecosystems. (shrink)

Cancers rely on multiple, heterogeneous processes at different scales, pertaining to many biomedical fields. Therefore, understanding cancer is necessarily an interdisciplinary task that requires placing specialised experimental and clinical research into a broader conceptual, theoretical, and methodological framework. Without such a framework, oncology will collect piecemeal results, with scant dialogue between the different scientific communities studying cancer. We argue that one important way forward in service of a more successful dialogue is through greater integration of applied sciences (experimental and clinical) (...) with conceptual and theoretical approaches, informed by philosophical methods. By way of illustration, we explore six central themes: (i) the role of mutations in cancer; (ii) the clonal evolution of cancer cells; (iii) the relationship between cancer and multicellularity; (iv) the tumour microenvironment; (v) the immune system; and (vi) stem cells. In each case, we examine open questions in the scientific literature through a philosophical methodology and show the benefit of such a synergy for the scientific and medical understanding of cancer. (shrink)

We offer a topological treatment of scattered theories intended to help to explain the parallelism between, on the one hand, the theorems provable using Descriptive Set Theory by analysis of the space of countable models and, on the other, those provable by studying a tree of theories in a hierarchy of fragments of infinintary logic. We state some theorems which are, we hope, a step on the road to fully understanding counterexamples to Vaught's Conjecture. This framework is in the early (...) stages of development, and one area for future exploration is the possibility of extending it to a setting in which the spaces of types of a theory are uncountable. (shrink)

Traditional outcome-orientated egalitarian principles require access to information about the size of individual holdings. Recent egalitarian political theory has sought to accommodate considerations of responsibility. Such a move may seem problematic, in that a new informational burden is thereby introduced, with no apparent decrease in the existing burden. This article uses a simple model with simulated data to examine the extent to which outcome egalitarianism and responsibility-sensitive egalitarianism (‘luck egalitarianism’) can be accurately applied where information is incomplete or erroneous. It (...) is found that, while outcome egalitarianism tends to be more accurately applied, its advantage is not overwhelming, and in many prima facie plausible circumstances luck egalitarianism would be more accurately applied. This suggests that luck egalitarianism cannot be rejected as utopian. Furthermore, while some argue that, in practice, luck egalitarianism is best realized indirectly, by securing equality of outcome, our evidence suggests that a luck egalitarian rule of regulation offers a far more accurate implementation of the luck egalitarian ideal than does an outcome egalitarian rule of regulation. (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)

Despite the evidence showing the promise of HIV treatment as prevention (TasP) in reducing HIV incidence, a variety of ethical questions surrounding the implementation and “scaling up” of TasP have been articulated by a variety of stakeholders including scientists, community activists and government officials. Given the high profile and potential promise of TasP in combatting the global HIV epidemic, an explicit and transparent research priority-setting process is critical to inform ongoing ethical discussions pertaining to TasP.

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).

Burgess, J.P. and Rosen, G. Subject with No ObjectElliott, R.Faking Nature.

Philosophical arguments stemming from the public health ethics arena suggest that public health interventions ought to be subject to normative inquiry that considers relational values, including concepts such as solidarity, reciprocity and health equity. As yet, however, the extent to which ‘public’ values influence the ‘autonomous’ decisions of the public remains largely unexplored. Drawing on interviews with 50 men in Vancouver, Canada, this study employs a critical discourse analysis to examine participants’ decisions and motivations to voluntarily access HIV testing and/or (...) to accept a routine HIV test offer. Within a sub-set of interviews, a transactional discourse emerged in which the decision to test features an arrangement of ‘giving and receiving’. Discourses related to notions of solidarity emphasize considerations of justice and positions testing as a ‘public’ act. Lastly, ‘individualistic’ discourses focused on individual-level considerations, with less concern for the broader public ‘good’. These findings underscore how normative dimensions pertaining to men’s decisions to test are dialectically interrelated with the broader social and structural influences on individual and collective health-related behaviour, thereby suggesting a need to advance an explicit empirical-normative research agenda related to population and public health intervention research. (shrink)