Modelling biological complexity: a physical scientist's perspective.
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We discuss the modern approaches of complexity and self-organization to understanding dynamical systems and how these concepts can inform current interest in systems biology. From the perspective of a physical scientist, it is especially interesting to examine how the differing weights given to philosophies of science in the physical and biological sciences impact the application of the study of complexity. We briefly describe how the dynamics of the heart and circadian rhythms, canonical examples of systems biology, are modelled by sets of nonlinear coupled differential equations, which have to be solved numerically. A major difficulty with this approach is that all the parameters within these equations are not usually known. Coupled models that include biomolecular detail could help solve this problem. Coupling models across large ranges of length- and time-scales is central to describing complex systems and therefore to biology. Such coupling may be performed in at least two different ways, which we refer to as hierarchical and hybrid multiscale modelling. While limited progress has been made in the former case, the latter is only beginning to be addressed systematically. These modelling methods are expected to bring numerous benefits to biology, for example, the properties of a system could be studied over a wider range of length- and time-scales, a key aim of systems biology. Multiscale models couple behaviour at the molecular biological level to that at the cellular level, thereby providing a route for calculating many unknown parameters as well as investigating the effects at, for example, the cellular level, of small changes at the biomolecular level, such as a genetic mutation or the presence of a drug. The modelling and simulation of biomolecular systems is itself very computationally intensive; we describe a recently developed hybrid continuum-molecular model, HybridMD, and its associated molecular insertion algorithm, which point the way towards the integration of molecular and more coarse-grained representations of matter. The scope of such integrative approaches to complex systems research is circumscribed by the computational resources available. Computational grids should provide a step jump in the scale of these resources; we describe the tools that RealityGrid, a major UK e-Science project, has developed together with our experience of deploying complex models on nascent grids. We also discuss the prospects for mathematical approaches to reducing the dimensionality of complex networks in the search for universal systems-level properties, illustrating our approach with a description of the origin of life according to the RNA world view. (+info)
Accessing bioscience images from abstract sentences.
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Images (e.g., figures) are important experimental results that are typically reported in bioscience full-text articles. Biologists need to access images to validate research facts and to formulate or to test novel research hypotheses. On the other hand, biologists live in an age of information explosion. As thousands of biomedical articles are published every day, systems that help biologists efficiently access images in literature would greatly facilitate biomedical research. We hypothesize that much of image content reported in a full-text article can be summarized by the sentences in the abstract of the article. In our study, more than one hundred biologists had tested this hypothesis and more than 40 biologists had evaluated a novel user-interface BioEx that allows biologists to access images directly from abstract sentences. Our results show that 87.8% biologists were in favor of BioEx over two other baseline user-interfaces. We further developed systems that explored hierarchical clustering algorithms to automatically identify abstract sentences that summarize the images. One of the systems achieves a precision of 100% that corresponds to a recall of 4.6%. (+info)
Gender differences in patenting in the academic life sciences.
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We analyzed longitudinal data on academic careers and conducted interviews with faculty members to determine the scope and causes of the gender gap in patenting among life scientists. Our regressions on a random sample of 4227 life scientists over a 30-year period show that women faculty members patent at about 40% of the rate of men. We found that the gender gap has improved over time but remains large. (+info)
Meeting report: teaching signal transduction.
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In July, 2005, the European Institute of Chemistry and Biology at the campus of the University of Bordeaux, France, hosted a focused week of seminars, workshops, and discussions around the theme of "teaching signal transduction." The purpose of the summer school was to offer both junior and senior university instructors a chance to reflect on the development and delivery of their teaching activities in this area. This was achieved by combining open seminars with restricted access workshops and discussion events. The results suggest ways in which systems biology, information and communication technology, Web-based investigations, and high standard illustrations might be more effectively and efficiently incorporated into modern cell biology courses. (+info)
The physician-scientist, the state, and the oath: thoughts for our times.
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Triggered by an encounter with survivors of the studies on twins conducted in Auschwitz by Joseph Mengele, who held both MD and PhD degrees, I offer thoughts on the extraordinary powers physician-scientists have to enhance or degrade human dignity. Biomedical science lacks intrinsic morality, but attains moral status by virtue of its purpose and the ethical framework that controls its conduct, both of which derive from the principles of medical humanism codified in the physician's oath. Physician-scientists have responsibilities to humankind that transcend the state. Careful analysis of historical examples of abuses of human rights committed in the name of medical science or the state is an important mechanism to safeguard current and future human participants. (+info)
Nanotechnology: the next big thing, or much ado about nothing?
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Nanotechnology encompasses an increasingly sophisticated ability to manipulate matter at the nanoscale, resulting in new materials, products and devices that demonstrate new and unusual behaviour. While emerging nanotechnologies have great potential for good, there are increasing concerns that the selfsame attributes that make them attractive will also lead to new risks to human health. Research to date suggests that some purposely made nanomaterials will present hazards based on their structure--as well as their chemistry--thus challenging many conventional approaches to risk assessment and management. People involved in making and using these materials need to know what the risks are and how to manage them, if safe nanotechnology-based businesses are to emerge. Yet the challenges faced by the occupational hygiene community in ensuring safe nano-workplaces are substantial. We currently know enough to suggest that some engineered nanomaterials will present new and unusual risks, but there is very little information on how these risks can be identified, assessed and controlled. And many nanomaterials are in production and use now. Good occupational hygiene practices and existing knowledge on working with hazardous substances provide a useful basis for working safely with nanomaterials. But where existing knowledge fails, new research is needed to fill the gaps: this must be strategically administered and targeted to addressing specific issues in a timely manner. Failing to take these steps will ultimately lead to people's health being endangered and emerging nanotechnologies floundering. However, with foresight, sound science and strategic research, we have the opportunity to ensure that emerging nanotechnologies are as safe as possible, while reaching their full potential. (+info)
Teaching aldosterone regulation and basic scientific principles using a classic paper by Dr. James O. Davis and colleagues.
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Classroom discussion of scientific articles can be an effective means of teaching scientific principles and methodology to both undergraduate and graduate science students. The availability of classic papers from the American Physiological Society Legacy Project has made it possible to access articles dating back to the early portions of the 20th century. In this article, we discuss a classic paper from the laboratory of Dr. James O. Davis on the regulation of aldosterone synthesis from the adrenal zona glomerulosa cell. Dr. Davis has conducted much of the seminal research investigating the renin-angiotensin system and the regulation of aldosterone release by angiotensin II. In addition to a characterization of the effects of ACTH on aldosterone regulation, this study is useful for discussing the basic principles of negative feedback pathways of the hypothalamic-pituitary axis. This study also provides examples of early bioassay techniques for the detection of angiotensin II and of the importance of quantitative measurements when investigating physiological responses. Three figures and one table are reproduced from the original article along with a series of discussion questions designed to facilitate discovery learning. (+info)
NASA--has its biological groundwork for a trip to Mars improved?
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In a 1991 editorial in The FASEB Journal, Robert W. Krauss commented on a recent report of the Presidential Advisory Committee on the Future of the U.S. Space Program (Augustine report). He concluded that, although a manned mission to Mars with life sciences as the priority was endorsed by the Committee, it failed to deal realistically with one huge gap; biological sciences have never been given high priority. According to Krauss, this left a void that will cripple, perhaps fatally, any early effort to ensure long-term survival on any mission of extended duration. The gap included insufficient flight time for fundamental biological space research and insufficient funds. Krauss expressed his opinions 15 years ago. Have we better knowledge of space biology now? This question becomes more acute now that President George W. Bush recently proposed a manned return to the moon by 2015 or 2020, with the moon to become our staging post for manned missions to Mars. Will we be ready so soon? A review of the progress in the last 15 years suggests that we will not. Because of the Columbia disaster, flight opportunities for biological sciences in shuttle spacelabs and in Space Station laboratories compete with time for engineering problems and construction. Thus, research on gravity, radiation, and isolation loses out to problems deemed to be of higher priority. Radiation in deep space and graded gravity in space with on board centrifuges are areas that must be studied before we undertake prolonged space voyages. Very recent budgetary changes within National Aeronautics and Space Administration threaten to greatly reduce the fundamental space biology funds. Are we ready for a trip to Mars? Like Krauss 15 years ago, I think not for some time. (+info)