S. K. Sarkar

© 2015.This document a59Summary of the discussions and conclusions following from Dark Matter @ LHC 2014, held at Merton College, Oxford, on September 25-27, 2014. outlines a set of simplified models for dark matter and its interactions with Standard Model particles. It is intended to summarize the main characteristics that these simplified models have when applied to dark matter searches at the LHC, and to provide a number of useful expressions for reference. The list of models includes both s-channel and t-channel scenarios. For s-channel, spin-0 and spin-1 mediations are discussed, and also realizations where the Higgs particle provides a portal between the dark and visible sectors. The guiding principles underpinning the proposed simplified models are spelled out, and some suggestions for implementation are presented.

The ongoing controversy about the possibility of directed mutations in bacteria is examined for its methodological, and thereby philosophical, implications. The method of fluctuation analysis, widely used to investigate whether mutations are random or directed, is described and subjected to a conceptual critique which shows that it cannot decide whether some mutations are directed while most are random. In this context, recent experiments that exploit this possibility to suggest that directed mutations occur in bacteria are described. Interpretive and experimental responses to such claims are briefly analyzed. Finally it is argued that mere statistical analysis, such as fluctuation analysis, cannot resolve this dispute. What will probably be required is an investigation of mechanisms of mutagenesis, an investigation that is intrinsically reductive.

It is shown that, for technical reasons, the additivity of variance criterion employed by Lloyd (1988) to define a unit of selection is, in almost all models of selection, inconsistent with the possibility that genes are sometimes not the unit of selection. A case when the latter view is particularly attractive is that of heterosis, and the additivity criterion is inadequate in even such an extreme case. The connection between that criterion and the so-called "fundamental theorem of natural selection" is briefly explored. Skepticism is expressed about the value of measures such as variance in efforts to resolve any of the disputes about the "units of selection.".

Explicit, quantitative procedures for identifying biodiversity priority areas are replacing the often ad hoc procedures used in the past to design networks of reserves to conserve biodiversity. This change facilitates more informed choices by policy makers, and thereby makes possible greater satisfaction of conservation goals with increased efficiency. A key feature of these procedures is the use of the principle of complementarity, which ensures that areas chosen for inclusion in a reserve network complement those already selected. This paper sketches the historical development of the principle of complementarity and its applications in practical policy decisions. In the first section a brief account is given of the circumstances out of which concerns for more explicit systematic methods for the assessment of the conservation value of different areas arose. The second section details the emergence of the principle of complementarity in four independent contexts. The third section consists of case studies of the use of the principle of complementarity to make practical policy decisions in Australasia, Africa, and America. In the last section, an assessment is made of the extent to which the principle of complementarity transformed the practice of conservation biology by introducing new standards of rigor and explicitness.

A standard norm of reaction (NoR) is a graphical depiction of the phenotypic value of some trait of an individual genotype in a population as a function of an environmental parameter. NoRs thus depict the phenotypic plasticity of a trait. The topological properties of NoRs for sets of different genotypes can be used to infer the presence of (non-linear) genotype-environment interactions. While it is clear that many NoRs are adaptive, it is not yet settled whether their evolutionary etiology should be explained by selection on the mean phenotypic trait values in different environments or whether there are specific genes conferring plasticity. If the second alternative is true the NoR is itself an object of selection. Generalized NoRs depict plasticity at the level of populations or subspecies within a species, species within a genus, or taxa at higher levels. Historically, generalized NoRs have routinely been drawn though rarely explicitly recognized as such. Such generalized NoRs can be used to make evolutionary inferences at higher taxonomic levels in a way analagous to how standard NoRs are used for microevolutionary inferences.

Newman objects to human germ-line editingGerm-line editing on both philosophical and practical grounds. While the philosophical grounds are compelling, I argue that they are not sufficiently strong to exclude all germ-line editingGerm-line editing to eliminate genetic diseasesGenetic disease. However, the practical reasons he offers preclude germ-line editing except in very limited circumstances. I argue that my requirement of gene specificityGene specificity in Cut-and-Paste Genetics can address his concerns. Meanwhile Baxter argues that my criteria are so restrictive that they would exclude all presently plausible candidate genes from being edited in the human germ-line editingGerm-line editing. I agree that this may be the case but that it is an acceptable policy situation because it behooves us to be very careful when editing of the human germ-line is at stake.

The emergence of CRISPR/Cas9 technology has revolutionized gene editing and made both gene therapy and eugenic control of future human evolution plausible. This accessible book puts these developments in their historical and scientific contexts and analyzes the policy and ethical challenges they raise. It presents the case for altering the human germ-line to eliminate a large number of genetic diseases controlled by a single or few genes, while pointing out that gene therapy is likely to ineffective for diseases with more complex causation. In parallel it explores the possibility of genetic enhancement in a similarly subscribed set of cases. But it also argues that, in general, genetic enhancement is ethically problematic and should be approached with caution. Given the success of CRISPR/Cas9 gene editing, and the explosion of related techniques, in practice it would be virtually impossible to ban germ-line editing for the future. A more useful goal is to regulate it with oversight that represents all stakeholders. That, in turn, requires an informed public discussion of these issues which this book aims to foster.

The emergence of CRISPR/Cas9 technology has revolutionized gene editing and made both gene therapy and eugenic control of future human evolution plausible. This accessible book puts these developments in their historical and scientific contexts and analyzes the policy and ethical challenges they raise. It presents the case for altering the human germ-line to eliminate a large number of genetic diseases controlled by a single or few genes, while pointing out that gene therapy is likely to ineffective for diseases with more complex causation. In parallel it explores the possibility of genetic enhancement in a similarly subscribed set of cases. But it also argues that, in general, genetic enhancement is ethically problematic and should be approached with caution. Given the success of CRISPR/Cas9 gene editing, and the explosion of related techniques, in practice it would be virtually impossible to ban germ-line editing for the future. A more useful goal is to regulate it with oversight that represents all stakeholders. That, in turn, requires an informed public discussion of these issues which this book aims to foster.

Comprised of essays by top scholars in the field, this volume offers detailed overviews of philosophical issues raised by biology. Brings together a team of eminent scholars to explore the philosophical issues raised by biology Addresses traditional and emerging topics, spanning molecular biology and genetics, evolution, developmental biology, immunology, ecology, mind and behaviour, neuroscience, and experimentation Begins with a thorough introduction to the field Goes beyond previous treatments that focused only on evolution to give equal attention to other areas, such as molecular and developmental biology Represents both an authoritative guide to philosophy of biology, and an accessible reference work for anyone seeking to learn about this rapidly-changing field.

Biological diversity - or ‘biodiversity’ - is the degree of variation of life within an ecosystem. It is a relatively new topic of study but has grown enormously in recent years. Because of its interdisciplinary nature the very concept of biodiversity is the subject of debate amongst philosophers, biologists, geographers and environmentalists. The Routledge Handbook of Philosophy of Biodiversity is an outstanding reference source to the key topics and debates in this exciting subject. Comprising twenty-three chapters by a team of international contributors the _Handbook_ is divided into six parts: Historical and sociological contexts, focusing on the emergence of the term and early attempts to measure biodiversity _What is biodiversity? _How should biodiversity be defined? How can biodiversity include entities at the edge of its boundaries, including microbial diversity and genetically engineered organisms? _Why protect biodiversity? _What can traditional environmental ethics_ _contribute to biodiversity?_ _Topics covered include anthropocentrism, intrinsic value, and ethical controversies surrounding the economics of biodiversity _Measurement and methodology: _including decision-theory and conservation, the use of indicators for biodiversity, and the changing use of genetics in biodiversity conservation _Social contexts and global justice: _including conservation and community conflicts and biodiversity and cultural values _Biodiversity and other environmental values_: How does biodiversity relate to other values like ecological restoration or ecological sustainability? Essential reading for students and researchers in philosophy, environmental science and environmental studies, and conservation management, it will also be extremely useful to those studying biodiversity in subjects such as biology and geography.

This book explores the epistemological and ethical issues at the foundations of environmental philosophy, emphasising the conservation of biodiversity. Sahota Sarkar criticises attempts to attribute intrinsic value to nature and defends an anthropocentric position on biodiversity conservation based on an untraditional concept of transformative value. Unlike other studies in the field of environmental philosophy, this book is as much concerned with epistemological issues as with environmental ethics. It covers a broad range of topics, including problems of explanation and prediction in traditional ecology and how individual-based models and Geographic Information Systems technology is transforming ecology. Introducing a brief history of conservation biology, Sarkar analyses the consensus framework for conservation planning through adaptive management. He concludes with a discussion of directions for theoretical research in conservation biology and environmental philosophy.

A recent set of experiments by Cairnset al.(1988) purport to show that some mutations in a strain ofE. colibacteria are directed in the sense that they are induced, somehow, in an environment that is suited for them. If this claim is true it would limit the validity of the neo-Darwinian assumption that evolution proceeds by “random variation and natural selection” which requires that there be no correlation between the genesis of a particular mutation and the fitness of the corresponding phenotype in the environment in which the mutation occurs. Instead, it would argue for the occurrence of some “neo-Lamarckian” processes in evolution in the sense that the genesis of some mutations would have a positive correlation with the fitness of the resultant phenotype in that environment. Thus, one of the most fundamental tenets of the neo-Darwinian interpretation of evolution would be brought into question.

Over the last eighteen years Manfred Eigen and his co-workers have postulated a new theory about the origin of life on earth that has presented a detailed account of how many of the features of extant living organisms (such as a universal genetic code and protein-nucleic acid interdependence) might have arisen from purely physical interactions.2 This theory is critically based on the special dynamical properties of certain chemical cycles called “hypercycles” which cause some of them to exhibit hyperbolic growth over time while undergoing selection. The purpose of this paper is to separate two aspects of this theory and then to study the first one in greater detail. The first aspect consists of a physical account of evolution by natural selection at the molecular level that depends only on the kinetics of certain chemical systems and can be applied to a variety of such systems. The second consists of the special dynamical properties that are exhibited when this account is applied, specifically, to hypercycles.

Despite the transformation in biological practice and theory brought about by discoveries in molecular biology, until recently philosophy of biology continued to focus on evolutionary biology. When the Human Genome Project got underway in the late 1980s and early 1990s, philosophers of biology -- unlike historians and social scientists -- had little to add to the debate. In this landmark collection of essays, Sahotra Sarkar broadens the scope of current discussions of the philosophy of biology, viewing molecular biology as a unifying perspective on life that complements that of evolutionary biology. His focus is on molecular biology, but the overriding question behind these papers is what molecular biology contributes to all traditional areas of biological research.Molecular biology -- described with some foresight in a 1938 Rockefeller Foundation report as a branch of science in which "delicate modern techniques are being used to investigate ever more minute details" -- and its modeling strategies apparently argue in favor of physical reductionism. Sarkar's first three chapters explore reductionism -- defending it, but cautioning that reduction to molecular interactions is not necessarily a reduction to genetics. The next sections of the book discuss function, exploring how functional explanations pose a problem for reductionism; the informational interpretation of biology and how it interacts with reductionism; and the tension between the unifying framework of molecular biology and the received framework of evolutionary theory. The concluding chapter is an essay in the emerging field of developmental evolution, exploring what molecular biology may contribute to the transformation of evolutionary theory as evolutionary theory takes into account morphogenetic development