Throughout the biological and biomedical sciences there is a growing need for, prescriptive ‘minimum information’ (MI) checklists specifying the key information to include when reporting experimental results are beginning to find favor with experimentalists, analysts, publishers and funders alike. Such checklists aim to ensure that methods, data, analyses and results are described to a level sufficient to support the unambiguous interpretation, sophisticated search, reanalysis and experimental corroboration and reuse of data sets, facilitating the extraction of maximum value from data sets (...) them. However, such ‘minimum information’ MI checklists are usually developed independently by groups working within representatives of particular biologically- or technologically-delineated domains. Consequently, an overview of the full range of checklists can be difficult to establish without intensive searching, and even tracking thetheir individual evolution of single checklists may be a non-trivial exercise. Checklists are also inevitably partially redundant when measured one against another, and where they overlap is far from straightforward. Furthermore, conflicts in scope and arbitrary decisions on wording and sub-structuring make integration difficult. This presents inhibit their use in combination. Overall, these issues present significant difficulties for the users of checklists, especially those in areas such as systems biology, who routinely combine information from multiple biological domains and technology platforms. To address all of the above, we present MIBBI (Minimum Information for Biological and Biomedical Investigations); a web-based communal resource for such checklists, designed to act as a ‘one-stop shop’ for those exploring the range of extant checklist projects, and to foster collaborative, integrative development and ultimately promote gradual integration of checklists. (shrink)

From the time of Descartes a strong tendency emerged to exclude the consideration of metaphysical questions as a necessary step towards developing truly scientific disciplines. Within human geography, positivism had a significant influence in moulding the discipline as "spatial science", resulting in a reductionist vision of humanity. Since the 1970s, in reaction to the limitations of this narrow vision and also to the deterministic perspective of marxism, humanistic approaches became important, but have failed to adequately deal with the exclusion of (...) metaphysical issues. The more recent emergence of postmodern influences within human geography, while being critical of the rigidities associated with Enlightenment thinking, and suggesting a greater tolerance of "difference", appears reluctant to reconsider the exclusion of metaphysics. This paper suggest that such a reconsideration could contribute significantly towards increasing human geography's capacity to help policy makers deal more adequately with some of the major issues facing humanity. (shrink)

Simple regression (regression analysis with a single explanatory variable), and multiple regression (regression models with multiple explanatory variables), typically correspond to very different biological questions. The former use regression lines to describe univariate associations. The latter describe the partial, or direct, effects of multiple variables, conditioned on one another. We suspect that the superficial similarity of simple and multiple regression leads to confusion in their interpretation. A clear understanding of these methods is essential, as they underlie a large range of (...) procedures in common use in biology. Beyond simple and multiple regression in their most basic forms, understanding the key principles of these procedures is critical to understanding, and properly applying, many methods, such as mixed models, generalised models, and causal inference using graphs (including path analysis and its extensions). A simple, but careful, look at the distinction between these two analyses is valuable in its own right, and can also be used to clarify widely-held misconceptions about collinearity (correlations among explanatory variables). There is no general sense in which collinearity is a problem. We suspect that the perception of collinearity as a hindrance to analysis stems from misconceptions about interpretation of multiple regression models, and so we pursue discussions about these misconceptions in this light. In particular, collinearity causes multiple regression coefficients to be less precisely estimated than corresponding simple regression coefficients. This should not be interpreted as a problem, as it is perfectly natural that direct effects should be harder to characterise than univariate associations. Purported solutions to the perceived problems of collinearity are detrimental to most biological analyses. (shrink)

Growing-Block theorists hold that past and present things are real, while future things do not yet exist. This generates a puzzle: how can Growing-Block theorists explain the fact that some sentences about the future appear to be true? Briggs and Forbes develop a modal ersatzist framework, on which the concrete actual world is associated with a branching-time structure of ersatz possible worlds. They then show how this branching structure might be used to determine the truth values of future contingents. They (...) point out three different ways of interpreting the logical connectives, which give rise to three different logics of the open future: one supervaluationist, one corresponding to Lukasiewicz's strong Kleene logic, and one intuitionist. (shrink)

We show that five important elements of the ‘nomological package’— laws, counterfactuals, chances, dispositions, and counterfactuals—needn’t be a problem for the Growing-Block view. We begin with the framework given in Briggs and Forbes (in The real truth about the unreal future. Oxford studies in metaphysics. Oxford University Press, Oxford, 2012 ), and, taking laws as primitive, we show that the Growing-Block view has the resources to provide an account of possibility, and a natural semantics for non-backtracking causal counterfactuals. We show (...) how objective chances might ground a more fine-grained concept of feasibility, and furnished a places in the structure where causation and dispositions might fit. The Growing-Block view, thus understood, provides the resources to explain the close link between modality and tense, so that it predicts modal change as time passes. This account lets us capture not only what the future might hold for us, and also what might have been. (shrink)

In a review of Frege's Puzzle1, Graeme Forbes makes the claim that Salmon's account of belief might be seen, under certain conditions, as a mere notational variant of a neo-Fregean theory; and thus that such an account might be reduced to a neo-Fregean one simply by rewriting it in terms of Fregean terminology. With a view to supporting his claim, Forbes offers an outline of an account of belief which, according to him, would satisfy the following conditions: (i) it (...) could be directly obtained from Salmon's own analysis by means of a certain set of substitutions, which presumably would not affect the essential features of Salmon's view; (ii) it could naturally be described as Fregean, in the sense that it would preserve, (at least) the spirit of Frege's doctrines, especially his fundamental intuitions about belief. Of course, the upshot of Forbes's argument is that Salmon's theory would not, at bottom, constitute a genuine alternative to a Fregean semantics for belief ascriptions. In this paper I argue to the effect that Forbes's claim is not in general sound. It seems to me that the sort of indirect argument used by Forbes - that of trying to undermine Salmon's theory by showing that it is just a version of a neo-Fregean account - does not provide someone working within a Fregean framework with an adequate strategy to counter Salmon's neo-Russellian views. It would perhaps be better to concentrate a Fregean attack on certain apparently dubious and highly controversial theses and results which are constitutive of Salmon's view, e.g. the counterintuitive character of a substantial set of consequences which follow from his theory of belief, as well as the associated revisionist stand he is forced to take towards our current patterns of speaking about belief. (shrink)

I explain and criticize a theory of beliefs and of belief sentences offered by Graeme Forbes. My main criticism will be directed at Forbes' idea that, as a matter of the semantic rules of belief reporting -- as a matter of the meaning of belief ascriptions -- to get at the subject's way of thinking in an attitude ascription, we must use expressions that are "linguistic counterparts" of the subject's expressions. I think we often do something like that, but (...) that we have other, equally good methods of getting at ways of thinking; so what is wanted is a more inclusive characterization of the rules of belief reporting by which we manage to do it -- a characterization more along the lines of: anything goes. (shrink)

Covers Essays 1 to 6 in Proclus' Commentary and includes a general introduction to the work as a whole.

What is a physical object according to the theory of quantum mechanics? The first answer to be considered is that given by Bohr in terms of the concept of complementarity. This interpretation is illustrated by way of an example, the two slit experiment, which highlights some of the associated problems of ontology. One such problem is the so-called problem of measurement or observation. Various interpretations of measurement in Quantum Theory, including those of Heisenberg, von Neumann, Everett and Bohr, are compared (...) and contrasted. A second problem concerns whether or not QT can be considered complete and therefore satisfactory as a basis for physics. Various attempts to complete QT by means of the addition of ‘hidden variables’ to the quantum mechanical state function are considered and their aims and achievements assessed. Finally, we investigate some of the characteristic ontological problems for the orthodox interpretation of Relativistic Quantum Theory. -/- . (shrink)

This book has been written for eighteen year olds (or anyone who will listen) as an honest attempt to face their justified questionings and to offer them a metaphysical framework with which to confront the twenty-first century. It is vitally important that certain modes of thought are uprooted and new modes put in their place if mankind and planet Earth are not soon to suffer an historic global catastrophe. Apart from the continuing world-wide proliferation of conventional, chemical, biological and nuclear (...) weaponry, the temperature of the planet has risen more rapidly in the last twenty-five years than it has since the year 900AD, which confirms global warming by some cause or other. These and the many intensifying human conflicts and natural disasters demand that some fundamental changes to our thinking are made as soon as possible. These 120 pages begin with an original examination of the quantum-theoretical understanding of reason (logic) and reality (existence) and find both to be at odds with common sense. A theory of everything is a reduction to a single grand idea! A quantum theory of everything is a mathematical theory of a consciousness realizing this grand idea! That is what this book tries to comprehend by means of five indisputable propositions. (shrink)