BackgroundThe ARRIVE (Animal Research: Reporting of In Vivo Experiments) guidelines are widely endorsed but compliance is limited. We sought to determine whether journal-requested completion of an ARRIVE checklist improves full compliance with the guidelines.MethodsIn a randomised controlled trial, manuscripts reporting in vivo animal research submitted to PLOS ONE (March–June 2015) were randomly allocated to either requested completion of an ARRIVE checklist or current standard practice. Authors, academic editors, and peer reviewers were blinded to group allocation. Trained reviewers performed outcome adjudication (...) in duplicate by assessing manuscripts against an operationalised version of the ARRIVE guidelines that consists 108 items. Our primary outcome was the between-group differences in the proportion of manuscripts meeting all ARRIVE guideline checklist subitems.ResultsWe randomised 1689 manuscripts (control: n = 844, intervention: n = 845), of which 1269 were sent for peer review and 762 (control: n = 340; intervention: n = 332) accepted for publication. No manuscript in either group achieved full compliance with the ARRIVE checklist. Details of animal husbandry (ARRIVE subitem 9b) was the only subitem to show improvements in reporting, with the proportion of compliant manuscripts rising from 52.1 to 74.1% (X2 = 34.0, df = 1, p = 2.1 × 10−7) in the control and intervention groups, respectively.ConclusionsThese results suggest that altering the editorial process to include requests for a completed ARRIVE checklist is not enough to improve compliance with the ARRIVE guidelines. Other approaches, such as more stringent editorial policies or a targeted approach on key quality items, may promote improvements in reporting. (shrink)

Hugo de Vries claimed that he had discovered Mendel's laws before he found Mendel's paper. De Vries's first ratios, published in 1897, for the second generation of hybrids were 2/3:1/3 and 80%:20%. By 1900, both of these ratios had become 3:1. These changing ratios suggest that as late as 1897 de Vries had not discovered the laws, although he asserted, from 1900 on, that he had found the laws in 1896. An Appendix details de Vries's Mendelian experiments as described in (...) the original edition of volume two of Die Mutationstheorie, but omitted entirely from the English translation. (shrink)

Summary The common view has been that Darwin regarded species as artificial and arbitrary constructions of taxonomists, not as distinct natural units. However, in his transmutation notebooks he clearly subscribed to the reality of species, on the basis of the criterion of non-interbreeding. A consequence of this biological species concept was his identification of the acquisition of reproductive isolation as the mark of the completion of speciation. He developed in the notebooks a theory of geographic speciation on the grounds of (...) (a) an empirical correlation between barriers and the geographical distributions of allied species, (b) the analogy of artificial isolation in the formation of new domesticated varieties, and (c) the logical consequence of blending inheritance. A brief discussion of Darwin's species concept in later writings concludes the paper. (shrink)

We lay groundwork for applying ethnographic methods in philosophy of science. We frame our analysis in terms of two tasks: to identify the benefits of an ethnographic approach in philosophy of science and to structure an ethnographic approach for philosophical investigation best adapted to provide information relevant to philosophical interests and epistemic values. To this end, we advocate for a purpose-guided form of cognitive ethnography that mediates between the explanatory and normative interests of philosophy of science, while maintaining openness and (...) independence when framing such an investigation to achieve robust unbiased results. (shrink)

In 1962 I offered an analysis of the Line and Cave which maintained that the four main divisions of each are parallel and interpreted the three stages of ascent in the Cave allegory as representing the three stages in Plato's educational programme: music and gymnastic, mathematics and dialectic. At that time a major portion of my task was to counter arguments which purported to show that the Line and Cave could not be parallel. The present situation is quite different since (...) recent writers, for the most part, not only take the four main divisions of the Cave as parallel to those of the Line, but also accept the restriction of the Cave allegory to moral and mathematical education as a crucial step in the establishing of this fact. This last move, which is clearly in harmony with the form and content of the Republic, enables us to allow for the ordinary unenlightened man to be at the bottom level of the Cave without our having to suggest that he confuses the shadows of visual objects with their originals, which could well be the case if the Cave were taken to represent all sense perception as such. Despite fairly general agreement on these basic points of interpretation there remains, however, a wide divergence of opinion as to the significance of the various levels of education or moral awareness portrayed by the Cave. In keeping with several recent papers on this topic I shall focus my attention on the bottom two stages of this allegory: the state of the prisoners viewing shadows on the cave wall and that of the released prisoners, still in the cave, but turned around and looking at the puppets which cast these shadows. (shrink)

A simple numerical procedure is presented for the problem of estimating the parameters of models for the distribution of eggs oviposited in a host. The modelling is extended to incorporate both host density and time dependence to produce a remarkably parsimonious structure with only seven parameters to describe a data set of over 3,000 observations. This is further refined using a mixed model to accommodate several large outliers. Both models show that the level of superparasitism declines with increasing host density, (...) and the rate declines over time. It is proposed that the differing behaviours represented by the mixed model may reflect a balance between behavioural strategies of different selective benefit. (shrink)

A judgement analysis of people's social inferences of attitudes and ability was conducted. University students were asked to infer the liberalness ( N = 60; Study 1) or intelligence ( N = 40; Study 2) of targets seen in pictures. Multiple regression analyses revealed that attractiveness was the most important cue for predicting inferences of liberalness, while an ethnic cue (i.e., being Asian) was the most important cue for judgements about intelligence. Results also showed that a single-cue model was less (...) susceptible to overfitting, but significantly less accurate than a multiple-cue model in predicting participant's intelligence judgements. Although the multiple regression models suffered a degree of overfitting, cross validation showed that they continued to have significant predictive value when applied to new data. Furthermore, a “random partner” method (comparing each participant's own regression equation with that of another, randomly selected, participant) provided evidence of significant idiosyncratic variation in the way intelligence judgements were made. (shrink)

When a study shows statistically significant correlation between an exposure and an outcome, the credence of a real connection between the two increases. Should that credence remain the same when it is discovered that further independent studies between the exposure and other independent outcomes were conducted? Matthew Kotzen argues that it should remain the same, even if the results of those further studies are discovered. However, we argue that it can differ dependent upon the results of the studies.

A simple numerical procedure is presented for the problem of estimating the parameters of models for the distribution of eggs oviposited in a host. The modelling is extended to incorporate both host density and time dependence to produce a remarkably parsimonious structure with only seven parameters to describe a data set of over 3,000 observations. This is further refined using a mixed model to accommodate several large outliers. Both models show that the level of superparasitism declines with increasing host density, (...) and the rate declines over time. It is proposed that the differing behaviours represented by the mixed model may reflect a balance between behavioural strategies of different selective benefit. (shrink)

ABSTRACTMany anti-bullying programmes use teachers in the critical role of provider, yet few trials focus on enhancing their ability to fulfil this role. As teachers’ readiness may impact on the ef...

Integrative systems biology is an emerging field that attempts to integrate computation, applied mathematics, engineering concepts and methods, and biological experimentation in order to model large-scale complex biochemical networks. The field is thus an important contemporary instance of an interdisciplinary approach to solving complex problems. Interdisciplinary science is a recent topic in the philosophy of science. Determining what is philosophically important and distinct about interdisciplinary practices requires detailed accounts of problem-solving practices that attempt to understand how specific practices address the (...) challenges and constraints of interdisciplinary research in different contexts. In this paper we draw from our 5-year empirical ethnographic study of two systems biology labs and their collaborations with experimental biologists to analyze a significant problem-solving approach in ISB, which we call adaptive problem solving. ISB lacks much of the methodological and theoretical resources usually found in disciplines in the natural sciences, such as methodological frameworks that prescribe reliable model-building processes. Researchers in our labs compensate for the lack of these and for the complexity of their problems by using a range of heuristics and experimenting with multiple methods and concepts from the background fields available to them. Using these resources researchers search out good techniques and practices for transforming intractable problems into potentially solvable ones. The relative freedom lab directors grant their researchers to explore methodological options and find good practices that suit their problems is not only a response to the complex interdisciplinary nature of the specific problem, but also provides the field itself with an opportunity to discover more general methodological approaches and develop theories of biological systems. Such developments in turn can help to establish the field as an identifiably distinct and successful approach to understanding biological systems. (shrink)

In this article, we provide a case study examining how integrative systems biologists build simulation models in the absence of a theoretical base. Lacking theoretical starting points, integrative systems biology researchers rely cognitively on the model-building process to disentangle and understand complex biochemical systems. They build simulations from the ground up in a nest-like fashion, by pulling together information and techniques from a variety of possible sources and experimenting with different structures in order to discover a stable, robust result. Finally, (...) we analyze the alternative role and meaning theory has in systems biology expressed as canonical template theories like Biochemical Systems Theory. (shrink)

The importation of computational methods into biology is generating novel methodological strategies for managing complexity which philosophers are only just starting to explore and elaborate. This paper aims to enrich our understanding of methodology in integrative systems biology, which is developing novel epistemic and cognitive strategies for managing complex problem-solving tasks. We illustrate this through developing a case study of a bimodal researcher from our ethnographic investigation of two systems biology research labs. The researcher constructed models of metabolic and cell-signaling (...) pathways by conducting her own wet-lab experimentation while building simulation models. We show how this coupling of experiment and simulation enabled her to build and validate her models and also triangulate and localize errors and uncertainties in them. This method can be contrasted with the unimodal modeling strategy in systems biology which relies more on mathematical or algorithmic methods to reduce complexity. We discuss the relative affordances and limitations of these strategies, which represent distinct opinions in the field about how to handle the investigation of complex biological systems. (shrink)

Modern integrative systems biology defines itself by the complexity of the problems it takes on through computational modeling and simulation. However in integrative systems biology computers do not solve problems alone. Problem solving depends as ever on human cognitive resources. Current philosophical accounts hint at their importance, but it remains to be understood what roles human cognition plays in computational modeling. In this paper we focus on practices through which modelers in systems biology use computational simulation and other tools to (...) handle the cognitive complexity of their modeling problems so as to be able to make significant contributions to understanding, intervening in, and controlling complex biological systems. We thus show how cognition, especially processes of simulative mental modeling, is implicated centrally in processes of model-building. At the same time we suggest how the representational choices of what to model in systems biology are limited or constrained as a result. Such constraints help us both understand and rationalize the restricted form that problem solving takes in the field and why its results do not always measure up to expectations. (shrink)

Integrative systems biology is among the most innovative fields of contemporary science, bringing together scientists from a range of diverse backgrounds and disciplines to tackle biological complexity through computational and mathematical modeling. The result is a plethora of problem-solving techniques, theoretical perspectives, lab-structures and organizations, and identity labels that have made it difficult for commentators to pin down precisely what systems biology is, philosophically or sociologically. In this paper, through the ethnographic investigation of two ISB laboratories, we explore the particular (...) structural features of ISB thinking and organization and its relations to other disciplines that necessitate cognitive innovation at all levels from lab PI’s to individual researchers. We find that systems biologists face numerous constraints that make the production of models far from straight-forward, while at the same time they inhabit largely unstructured task environments in comparison to other fields. We refer to these environments as adaptive problem spaces. These environments they handle by relying substantially on the flexibility and affordances of model-based reasoning to integrate these various constraints and find novel adaptive solutions. Ultimately what is driving this innovation is a determination to construct new cognitive niches in the form of functional model building frameworks that integrate systems biology within the biological sciences. The result is an industry of diverse and different innovative practices and solutions to the problem of modeling complex, large-scale biological systems. (shrink)

This book traces the intellectual revolution initiated by Thales in the sixth century BC to its culmination in the metaphysics of Parmenides.

In lieu of an abstract, here is a brief excerpt of the content:Comments on “Moral Complicity in Induced Pluripotent Stem Cell Research”W. Malcolm Byrnes, Ph.D. and Edward J. FurtonIn his article titled “Moral Complicity in Induced Pluripotent Stem Cell Research,” Mark T. Brown (2009) unfortunately mischaracterizes my ethical analysis of the use of induced pluripotent stem (iPS) cells for replacement therapies, or treatments (Byrnes 2008). In my paper, which Brown cites, I argue that, just as it is ethically acceptable (...) for parents to allow their children and themselves to be immunized using vaccines produced by cell lines derived from human fetuses aborted in the past, it is also acceptable for persons in the future to benefit from treatments that use iPS cells validated using human embryonic stem (ES) cell lines [End Page 202] derived in the past. The assumption I make is that iPS cells would have to be shown to be functionally equivalent to human ES cells—i.e., validated—before they could be used for cell replacement treatments. (If it turns out that this assumption is incorrect, and primate or even mouse ES cells can be used for the validation, then all residual ethical problems will disappear and there will be no ethical problems whatsoever associated with iPS cells.) I wrote:... [I]n both cases, the origin of the treatment is in a one-time event: either the one-time use of aborted fetuses to obtain cell lines (e.g., MRC-5 and WI- 38) to grow weakened virus strains for vaccine production, or the one-time destruction of human embryos to validate iPS cells, which then effectively replace embryonic stem cells. In the latter case, if no additional embryonic stem cell lines are derived, then derivation of the existing lines could be considered a “one-time” event in the past, albeit an event that extended over a several-year period(Byrnes 2008, p. 287, emphasis added).Note the phrase “if no additional embryonic stem cell lines are derived.” The derivation of ES cell lines inherently involves destruction of embryos; indeed, that is why many people, including me, are opposed to human ES cell research. In my article, I am arguing that, if no additional ES cell lines are derived, then no additional human embryos will be destroyed, and the destruction of human embryos will lie in the past. In this case, embryo destruction could be considered a past event, just as the abortion of a human fetus from which vaccine-producing cell lines were derived is a past, albeit tragic, event.In the process of building his argument that proponents of iPS cell research are morally complicit in embryo destruction, Brown (2009, p. 15) casts me as being in favor of the “derivation of new embryonic stem [cell lines].” This is the exact opposite of my position. In fact, I am opposed to further destruction of human embryos. I believe that the hundreds of ES cell lines already in existence are more than sufficient to validate iPS cells and so no additional lines need to be derived. This means that no additional human embryos will need to be destroyed.Apparently based on the misperception that I support future destruction of human embryos, Brown concludes that “Byrnes’s endorsement of ongoing iPSC validation studies would seem to implicate him and those who follow his lead in formal and material complicity in what they perceive as moral evil” (p. 16). He writes that “explicit formal complicity would attach because he [Byrnes] knowingly and intentionally recommends that embryos be killed in order to facilitate a transition to a future in which no more embryos need be destroyed” (p. 16). Additionally, my “followers” and I would be guilty of “proximate material complicity” as well as “remote material complicity” (p. 16). Unfortunately, this broad condemnation is based on a misconception of my actual position.An additional problem involves Brown’s use of a quotation he attributes to me: [End Page 203]Once embryonic stem cells are used to successfully validate iPS cells, they will no longer be needed and their association with iPS cells will lie in the past. Is there not an element of sadness and resignation in accepting something (iPS cells) associated with an unjust act (destruction of an... (shrink)

Despite the known positive effects of acute exercise on cognition, the effects of a competitive team sport match are unknown. In a randomized crossover design, 20 female and 17 male field hockey players completed a battery of cognitive tests prior to, at half-time, and immediately following a competitive match ; with effect sizes presented as raw ES from mixed effect models. Blood samples were collected prior to and following the match and control trial, and analyzed for adrenaline, noradrenaline, brain derived (...) neurotrophic factor, cathepsin B, and cortisol. The match improved response times for a simple perception task at full-time and response times on the complex executive function task improved at half-time. Working memory declined at full-time on the match. The change in working memory was negatively correlated with increases in cortisol, as was the change in simple perception response time and the change in noradrenaline concentration. This study is the first to highlight the effects a competitive hockey match can have on cognition. These findings have implications for performance optimization, as understanding the influence on specific cognitive domains across a match allows for the investigation into strategies to improve these aspects. (shrink)