Can we make sense of subjective experience in metabolically situated cognitive processes?

In “Mind, matter and metabolism,” Godfrey-Smith’s objective is to “develop a picture” in which, first, the basis of living activity in physical processes “makes sense,” second, the basis of proto-cognitive activity in living activity “makes sense” and third, “the basis of subjective experience in metabolically situated cognitive processes also makes sense.” show that he fails to attain all three of these objectives, largely owing to the nature and modularization of metabolism.     

Can tourism make a major contribution to the conservation of protected areas in Madagascar?

The authors review the anticipated benefits from tourism for protected areas in Madagascar, the mechanisms that have been adopted, and how these are working at national and local levels. The contribution of tourism to the maintenance of Protected Areas in Madagascar is assessed. The anticipated benefits of tourism envisaged by the 1991 National Environmental Action Plan are considered to be over-optimistic. The growth rate in tourist arrivals is found to be smaller than previously anticipated as a result of infrastructural constraints at national and local scales. It is suggested that revenues from tourism are inadequate in meeting park management costs although the local transfer of entrance fee revenues to development projects is found to be more beneficial. It is also argued that the benefits of revenue sharing can be effective only for a limited number of protected areas until unfrastructure is improved and protected areas become more accessible to tourists.     

Can we detect the development of baroreflex sensitivity in humans between 11 and 20 years of age?

The aim of the study was to determine changes of baroreflex sensitivity in humans between 11 and 20 years of age. Continuous 5 min blood pressure recordings using a Finapres were taken in 415 healthy subjects while in a sitting, resting position (breathing at a frequency of 0.33 Hz). Beat-by-beat values of interbeat intervals (IBI) or heart rate, and systolic and diastolic blood pressures were measured. Baroreflex sensitivity in ms/mmHg (BRS) and in mHz/mmHg (BRSf) was determined at an average frequency of 0.1 Hz by spectral analysis. BRS did not correlate with age, but BRSf significantly decreased with age (p < 0.001). BRS correlated with mean IBI (p < 0.001) in all subjects and also in the particular subgroups, but BRSf was IBI-independent. Results of multiregression equations were BRS = 1.37 - 0.56 x age (years) + 0.02 x IBI (ms) (p < 0.001 for BRS vs. age and for BRS vs. IBI); BRSf = 34.74 - 0.97 x age (years) - 0.001 x IBI (ms) (p < 0.001 only for BRS vs. age), where age was measured in years and IBI was measured in ms. The limits of BRS were estimated for the total group: 5th percentile, 3.9; 50th percentile, 9.1; and 95th percentile, 18.7 ms/mmHg; and limits for BRSf were 5th percentile, 8.5; 50th percentile, 16.4; and 95th percentile, 33.6 mHz/mmHg. We conclude that IBI-dependent BRS was unchanged in the particular age groups, but the standardization of BRS on IBI decreased with age. BRSf was IBI-independent and better reflected the development of the BRS.     

DNA repair in Mycobacterium tuberculosis. What have we learnt from the genome sequence?

The genome sequence of Mycobacterium tuberculosis was analysed by searching for homologues of genes known to be involved in the reversal or repair of DNA damage in Escherichia coli and related organisms. Genes necessary to perform nucleotide excision repair (NER), base excision repair (BER), recombination, and SOS repair and mutagenesis were identified. In particular, all of the genes known to be directly involved in the repair of oxidative and alkylative damage are present in M. tuberculosis . In contrast, we failed to identify homologues of genes involved in mismatch repair. This finding has potentially significant implications with respect to genome stability, strain variability at repeat loci and the emergence of chromosomally encoded drug resistance mutations.     

Can we stop transgenes from taking a walk on the wild side?

Whether the potential costs associated with broad‐scale use of genetically modified organisms (GMOs) outweigh possible benefits is highly contentious, including within the scientific community. Even among those generally in favour of commercialization of GM crops, there is nonetheless broad recognition that transgene escape into the wild should be minimized. But is it possible to achieve containment of engineered genetic elements in the context of large scale agricultural production? In a previous study, Warwick et al. (2003) documented transgene escape via gene flow from herbicide resistant (HR) canola (Brassica napus) into neighbouring weedy B. rapa populations ( Fig. 1 ) in two agricultural fields in Quebec, Canada. In a follow‐up study in this issue of Molecular Ecology, Warwick et al. (2008) show that the transgene has persisted and spread within the weedy population in the absence of selection for herbicide resistance. Certainly a trait like herbicide resistance is expected to spread when selected through the use of the herbicide, despite potentially negative epistatic effects on fitness. However, Warwick et al.'s findings suggest that direct selection favouring the transgene is not required for its persistence. So is there any hope of preventing transgene escape into the wild?

Figure 1 Open in figure viewer PowerPoint Weedy Brassica rapa (orange flags) growing in a B. napus field. (Photo: MJ Simard)     

Can a 'patch' in a skipped exon make the pre-mRNA splicing machine run better?

It is becoming clear that exonic sequences can act as determinants of their own fate: the inclusion or exclusion from mature mRNA. Indeed, even silent nucleotide substitutions can cause aberrant exon skipping, resulting in a disease phenotype. It might be possible to restore essential splicing functions, lost through mutations, using molecular therapy at the RNA level. A variety of methods have been attempted, the most promising being the recent use of chimeric compounds that localize splicing-functional peptides by base complementarity.     

Can enzyme engineering benefit from the modulation of protein motions? Lessons learned from NMR relaxation dispersion experiments

Despite impressive progress in protein engineering and design, our ability to create new and efficient enzyme activities remains a laborious and time-consuming endeavor. In the past few years, intricate combinations of rational mutagenesis, directed evolution and computational methods have paved the way to exciting engineering examples and are now offering a new perspective on the structural requirements of enzyme activity. However, these structure-function analyses are usually guided by the time-averaged static models offered by enzyme crystal structures, which often fail to describe the functionally relevant 'invisible states' adopted by proteins in space and time. To alleviate such limitations, NMR relaxation dispersion experiments coupled to mutagenesis studies have recently been applied to the study of enzyme catalysis, effectively complementing 'structure-function' analyses with 'flexibility-function' investigations. In addition to offering quantitative, site-specific information to help characterize residue motion, these NMR methods are now being applied to enzyme engineering purposes, providing a powerful tool to help characterize the effects of controlling long-range networks of flexible residues affecting enzyme function. Recent advancements in this emerging field are presented here, with particular attention to mutagenesis reports highlighting the relevance of NMR relaxation dispersion tools in enzyme engineering.     

Do we need a ‘theory’ of development?

Edited by Alessandro Minelli and Thomas Pradeu, Towards a Theory of Development gathers essays by biologists and philosophers, which display a diversity of theoretical perspectives. The discussions not only cover the state of art, but broaden our vision of what development includes and provide pointers for future research. Interestingly, all contributors agree that explanations should not just be gene-centered, and virtually none use design and other engineering metaphors to articulate principles of cellular and organismal organization. I comment in particular on the issue of how to construe the notion of a ‘theory’ and whether developmental biology has or should aspire to have theories, which four of the contributions discuss in detail while taking opposing positions. Beyond construing a theory in terms of its empirical content (established knowledge about biological phenomena), my aim is to shift the focus toward the role that theories have for guiding future scientific theorizing and practice. Such a conception of ‘theory’ is particularly important in the context of development, because arriving at a theoretical framework that provides guidance for the discipline of developmental biology as a whole is more plausible than a unified representation of development across all taxa.     

Synthesis of life in the lab? Defining a protoliving system

The synthesis of a living system in the lab has been judged by a number of critics as partly attained by the proteinoid microsphere because of its primitive properties of metabolism, growth, and reproduction. These same critics, however, judge the organism as not alive, or as being 50 to 75 percent alive (Baltscheffsky and Jurka, 1984), owing to the absence of a nucleic acid genetic coding mechanism. The experiments in retracing evolution suggest, however, that the self-sequencing of amino acids was the evolutionary precursor of modern nucleic acid templating; the genetic memory is the molecule. The proteinoid microsphere is not a modern living system, but does represent at least a protoliving system (Fox and Dose, 1972). Berra (1990, p. 75) has commented on other difficulties in defining a protoliving system. In Berra's opinion, metabolism, reproduction, responsiveness to stimuli, and cellularity constitute or describe aliveness. These properties characterize proteinoid microspheres. A number of experiments demonstrate that amino acids in aminoacyl adenylates yield specific products, whereas nucleotides are without effect. For this and related reasons, especially the demonstrated self-sequencing of amino acids when they are warmed, resultant bio-functional properties of self-assembled microstructures, and demonstrated self-sequencing of amino acids in modern systems, the results appear to bridge from the chemical era to the biological period. All the above emerges from a departure in style of research (Young, 1984; Pauling and Zuckerkandl, 1972). The latter authors said, "It appears likely that biogenesis is the passage from a 'non-living system' existing in a large number of states to a 'living' system also existing in a large number of states."(ABSTRACT TRUNCATED AT 250 WORDS)     

How accurate are population models? Lessons from landscape‐scale tests in a fragmented system

There is a growing debate about the ability of Population Viability Analysis (PVA) to predict the risk of extinction. Previously, the debate has focused largely on models where spatial variation and species movement are ignored. We present a synthesis of the key results for an array of different species for which detailed tests of the accuracy of PVA models were completed. These models included spatial variation in habitat quality and the movement of individuals across a landscape. The models were good approximations for some species, but poor for others. Predictive ability was limited by complex processes typically overlooked in spatial population models, these being interactions between landscape structure and life history attributes. Accuracy of models could not be determined a priori, although model tests indicated how they might be improved. Importantly, model predictions were poor for some species that are among the best‐studied vertebrates in Australia. This indicated that although the availability of good life history data is a key part of PVA other factors also influence model accuracy. We were also able to draw broad conclusions about the sorts of populations and life history characteristics where model predictions are likely to be less accurate. Predictions of extinction risk are often essential for real‐world population management. Therefore, we believe that although PVA has been shown to be less than perfect, it remains a useful tool particularly in the absence of alternative approaches. Hence, tests of PVA models should be motivated by the cycle of testing and improvement.     

Can we manage fisheries with the inherent uncertainty from eDNA?

Environmental (e)DNA, as a general approach in aquatic systems, seeks to connect the presence of species' genetic material in the water and hence to infer the species' physical presence. However, fisheries managers face making decisions with risk and uncertainty when eDNA indicates a fish is present but traditional methods fail to capture the fish. In comparison with traditional methods such as nets, electrofishing and piscicides, eDNA approaches have more sources of underlying error that could give rise to false positives. This has resulted in some managers to question whether eDNA can be used to make management decisions because there is no fish in hand. As a relatively new approach, the methods and techniques have quickly evolved to improve confidence in eDNA. By evaluating an eDNA based research programmes through the pattern of the eDNA signal, assay design, experimental design, quality assurance and quality control checks, data analyses and concurrent search for fish using traditional gears, the evidence for fish presence can be evaluated to build confidence in the eDNA approach. The benefits for fisheries management from adopting an eDNA approach are numerous but include cost effectiveness, broader geographic coverage of habitat occupancy, early detection of invasive species, non-lethal stock assessments, exploration of previously inaccessible aquatic environments and discovery of new species hidden beneath the water's surface. At a time when global freshwater and marine fisheries are facing growing threats from over-harvest, pollution and climate change, we anticipate that growing confidence in eDNA will overcome the inherent uncertainty of not having a fish in hand and will empower the informed management actions necessary to protect and restore our fisheries.     

Recalls of Cardiac Implants in the Last Decade: What Lessons Can We Learn?

Background

Due to an ageing population and demographic changes worldwide, a higher prevalence of heart disease is forecasted, which causes an even higher demand for cardiac implants in future. The increasing high incidence of clinical adverse events attributed especially to high-risk medical devices has led an advocated change from many stakeholders. This holds especially true for devices like cardiac implants, with their high-risk nature and high complication rates associated with considerable mortality, due to their frequent use in older populations with frequent co-morbidities. To ensure patients’ safety, the objective of this study is to analyze different cardiac implants recall reasons and different recall systems, based on an overview of the recalls of cardiac implant medical devices in the last decade. On the basis of the results from this structured analysis, this study provides recommendations on how to avoid such recalls from a manufacturer perspective, as well as how to timely react to an adverse event from a post-surveillance system perspective.

Methods and Findings

A systematic search of cardiac implant recalls information has been performed in the PubMed, ScienceDirect and Scopus databases, as well as data sources in regulatory authorities from 193 UN Member States. Data has been extracted for the years 2004-2014 with the following criteria applied: cardiac implant medical device recalls and reasons for recall, associated harm or risk to patients. From the data sources described above, eleven regulatory authorities and 103 recall reports have been included in this study. The largest cardiac implant categories include ICDs 40.8%, pacemakers 14.5% and stents 14.5%. Regarding the recall reasons, the majority of reports were related to device battery problems (33.0%) and incorrect therapy delivery (31.1%). From a total of 103 recall reports, five reported death and serious injuries. Our review highlights weaknesses in the current cardiac implant recall system, including data reporting and management issues and provides recommendations for the improvement of safety information and management.

Conclusion

Due to the mortality associated with the nature of cardiac implants, the traceability and transparency of safety hazards information is crucial. By a structured analysis of recall reasons and their efficient management, important knowledge is gained to inform an effective safety-reporting system for monitoring the safety of cardiac implanted patients, ideally by building up cardiac implant registries worldwide in the future.     

What are we to make of the concept of race?: Thoughts of a philosopher–scientist

Discussions about the biological bases (or lack thereof) of the concept of race in the human species seem to be never ending. One of the latest rounds is represented by a paper by Neven Sesardic, which attempts to build a strong scientific case for the existence of human races, based on genetic, morphometric and behavioral characteristics, as well as on a thorough critique of opposing positions. In this paper I show that Sesardic’s critique falls far short of the goal, and that his positive case is exceedingly thin. I do this through a combination of analysis of the actual scientific findings invoked by Sesardic and of some philosophical unpacking of his conceptual analysis, drawing on a dual professional background as an evolutionary biologist and a philosopher of science.     

Can monitoring data contribute to the biodiversity-ecosystem function debate? Evaluating data from a highly dynamic ecosystem

One of the most controversially discussed topics in current biodiversity-ecosystem function research is the transfer of results from experimental and theoretical studies to natural ecosystems. At the same time, monitoring data on biodiversity are requested as key indicators for the state of an ecosystem in most environmental evaluation frameworks. We analyse two monitoring data sets comprising information on abundance and biomass of macrozoobenthos communities in the German Wadden Sea in order to evaluate how much information monitoring data on biodiversity provide concerning ecosystem functioning and what implications this information (or the lack thereof) has for future monitoring programmes. Our results show a positive correlation between number of species of macrozoobenthos and its standing stock. Despite differences in overall biomass and individual size in different functional groups, this correlation remained consistent for different feeding guilds and therefore is likely to be independent of certain species traits. Moreover, functional turnover analyses indicate that increasing species richness is needed to maintain biomass levels over increasing periods of time. Whereas our data thus corroborate predictions from theory, we could not determine any causal relationships, because monitoring data commonly include only vague proxies for very few functional parameters, in our case standing biomass as a proxy for production. As to the use of diversity as an indicator for ecosystem functioning, we advise that management decisions are to be based on verified causal relationships and therefore strongly suggest the general incorporation of unambiguous proxies for functional parameters in the measuring campaigns of monitoring programmes.