Parsimony in evolutionary theory: Law or methodological prescription?

Parsimony (Ockham's razor) is in widespread use in phylogenetic reconstruction (evolution takes the shortest route), however it is not quite obvious which is the rank that this principle should have in evolutionary theory. Parsimony is not of a single kind but, on the contrary, is at least of two kinds: ontological and methodological. Ontological parsimony involves an assumption about the “simplicity of nature”. Methodological parsimony is a purely logical precept, a case of the broad practical principle not to believe anything for which there is no evidence. The two kinds of parsimony are not compatible with one another. The ontological hypotheses that reality is simple has been refuted many times in the history of science, and evolution is not an exception to this. In spite of the fact, that direct evolutionary changes have higher probability than the ones that take “unnecessary” steps, evolutionary parsimony is merely a methodological precept, not a law of evolution. Probability is not enough to give evolutionary parsimony a rank of ontological axiom. Therefore, the reasons to use the principle of evolutionary parsimony are only methodological. A definition of evolutionary parsimony is: as long as no evidence is available to suggest an alternative pathway evolution may be considered to occur in the most parsimonious way.     

Systems biology,emergence and antireductionism

This study explores the conceptual history of systems biology and its impact on philosophical and scientific conceptions of reductionism, antireductionism and emergence. Development of systems biology at the beginning of 21st century transformed biological science. Systems biology is a new holistic approach or strategy how to research biological organisms, developed through three phases. The first phase was completed when molecular biology transformed into systems molecular biology. Prior to the second phase, convergence between applied general systems theory and nonlinear dynamics took place, hence allowing the formation of systems mathematical biology. The second phase happened when systems molecular biology and systems mathematical biology, together, were applied for analysis of biological data. Finally, after successful application in science, medicine and biotechnology, the process of the formation of modern systems biology was completed.Systems and molecular reductionist views on organisms were completely opposed to each other. Implications of systems and molecular biology on reductionist–antireductionist debate were quite different. The analysis of reductionism, antireductionism and emergence issues, in the era of systems biology, revealed the hierarchy between methodological, epistemological and ontological antireductionism. Primarily, methodological antireductionism followed from the systems biology. Only after, epistemological and ontological antireductionism could be supported.     

Design and implementation of a mosquito database through an entomological ontology

There have been constant changes in the biology and behavior of the vector and parasite involved in the transmission of malaria. There is limited interest in developing new technologies and procedures for controlling the underlying factors of this threat, which poses an enormous challenge to health systems. To understand the various vector species and their interrelations is of prime importance in understanding the transmission mechanisms of malaria in order to react efficiently. To attain this objective, we have used an ontological approach to produce a database that we consider to be our own contribution in helping to control malarial vectors if eradication has been unsuccessful in the previous control campaign.     

Design and implementation of a mosquito database through an entomological ontology

There have been constant changes in the biology and behavior of the vector and parasite involved in the transmission of malaria. There is limited interest in developing new technologies and procedures for controlling the underlying factors of this threat, which poses an enormous challenge to health systems. To understand the various vector species and their interrelations is of prime importance in understanding the transmission mechanisms of malaria in order to react efficiently. To attain this objective, we have used an ontological approach to producing a database that we consider to be our own contribution in helping to control malaria vectors if eradication has been unsuccessful in the previous control campaign.     

OntoVisT: A general purpose Ontological Visualization Tool

Ontologies have emerged as a fast growing research topic in the area of semantic web during last decade. Currently there are 204 ontologies that are available through OBO Foundry and BioPortal. Several excellent tools for navigating the ontological structure are available, however most of them are dedicated to a specific annotation data or integrated with specific analysis applications, and do not offer flexibility in terms of general-purpose usage for ontology exploration. We developed OntoVisT, a web based ontological visualization tool. This application is designed for interactive visualization of any ontological hierarchy for a specific node of interest, up to the chosen level of children and/or ancestor. It takes any ontology file in OBO format as input and generates output as DAG hierarchical graph for the chosen query. To enhance the navigation capabilities of complex networks, we have embedded several features such as search criteria, zoom in/out, center focus, nearest neighbor highlights and mouse hover events. The application has been tested on all 72 data sets available in OBO format through OBO foundry. The results for few of them can be accessed through OntoVisT-Gallery. AVAILABILITY: The database is available for free at http://ccbb.jnu.ac.in/OntoVisT.html.     

‘The Earth Cannot Let Go of Us’: Analysing Ontological Conflicts

This paper examines certain key concepts of the ‘ontological turn’ in anthropology, with a view to a clearer understanding of its proposed methodology. It situates the ontological approach within the historical and intellectual conflicts through which it arose, outlining its motivations and the challenges it poses to traditional fieldwork methods and theory. The concepts of ‘radical alterity’ and ‘incommensurability’ are examined as intellectual as well as political concepts, highlighting their historical contingency on the politics of colonisation. Following from this, the notion of ‘ontological self-determination’ is analysed with respect to my fieldwork with the Dongria Kondh in the Niyamgiri Hills in Odisha, India; I show how an application of the ontological methodology allows a better understanding of certain conflicts within current discourses and practices of nationhood and development.     

Names,numbers and indentations: a guide to post-Linnaean taxonomy

The vast majority of biological taxonomists use the Linnaean system when constructing classifications. Taxa are assigned Linnaean ranks and taxon names are devised according to the Linnaean rules of nomenclature. Unfortunately, the Linnaean system has become theoretically outdated. Moreover, its continued use causes a number of practical problems. This paper begins by sketching the ontological and practical problems facing the Linnaean system. Those problems are sufficiently pressing that alternative systems of classification should be investigated. A number of proposals for an alternative system are introduced and evaluated. The best aspects of those proposals are brought together to form a post-Linnaean system, and a comparison of the Linnaean and post-Linnaean systems is conducted. The final section of this paper considers not only the theoretical reasons for replacing the Linnaean system, but also the practical feasibility of adopting an alternative system.     

Ontology of areas of endemism

Areas of endemism have been recognized as important units in historical biogeography, and much attention has been given to methods of identifying these units operationally. Interestingly, little has been written about the philosophical nature of areas of endemism. The purpose of this essay is to make an ontological argument for areas of endemism as individuals and to discuss the consequences of such a conclusion. The recognition of species as individuals is crucial to the argument. Several criteria are identified for entities to be considered individuals, all of which are shown for areas of endemism. An ontological concept of an area of endemism is presented. Two of the consequences of regarding areas of endemism as individuals are that areas of endemism should be the preferred units of biogeography over the units used in event‐based methods and that parsimony analysis of endemism and similar methods may be operational tools for the discovery of areas of endemism.     

Heterologous protein production and delivery systems for Lactococcus lactis

Lactic acid bacteria (LAB), widely used in the food industry, are present in the intestine of most animals, including humans. The potential use of these bacteria as live vehicles for the production and delivery of heterologous proteins of vaccinal, medical or technological interest has therefore been extensively investigated. Lactococcus lactis, a LAB species, is a potential candidate for the production of biologically useful proteins. Several delivery systems have been developed to target heterologous proteins to a specific cell location (i.e., cytoplasm, cell wall or extracellular medium). A promising application of L. lactis is its use as an antigen delivery vehicle, for the development of live mucosal vaccines. The expression of heterologous proteins and antigens as well as the various delivery systems developed in L. lactis, and its use as an oral vaccine carrier are discussed.     

Adaptation of wastewater surface flow wetland formulae for application in constructed stormwater wetlands

Over the past 30 years, the use of constructed wetlands for wastewater treatment has been a topic of significant research culminating in a good data base from which simplistic equations have been derived to aid in the design of these facilities to meet long term water quality treatment performance criteria. Over the past decade, the use of treatment wetlands has extended to stormwater and combined sewer overflow (CSO) management applications. Designing constructed wetlands for stormwater and CSO applications have unique challenges stemming from the highly stochastic nature of the hydraulic and pollutant loading on a stormwater wetland compared with wastewater treatment systems. This paper explores the possibility of adapting the simplistic models for wastewater wetlands for interim use in developing design guidelines for stormwater wetland systems. A procedure that takes into account the unsteady intermittent nature of stormwater inflows to these wetlands has been incorporated into one of these simplistic models and a case study presented to demonstrate the application of the procedure.     

Lactococcus lactis as a live vector: heterologous protein production and DNA delivery systems

Lactic acid bacteria (LAB), widely used in the food industry, are present in the intestine of most animals, including humans. The potential use of these bacteria as mucosal delivery vehicles for vaccinal, medical or technological use has been extensively investigated. Lactococcus lactis, a LAB species, is a potential candidate for the production of biologically useful proteins and for plasmid DNA delivery to eukaryotic cells. Several delivery systems have been developed to target heterologous proteins to a specific cell location (i.e., cytoplasm, cell wall or extracellular medium) and more recently to efficiently transfer DNA to eukaryotic cells. A promising application of L. lactis is its use for the development of live mucosal vaccines. Here, we have reviewed the expression of heterologous protein and the various delivery systems developed for L. lactis, as well as its use as an oral vaccine carrier.     

A knowledge model for analysis and simulation of regulatory networks

MOTIVATION: In order to aid in hypothesis-driven experimental gene discovery, we are designing a computer application for the automatic retrieval of signal transduction data from electronic versions of scientific publications using natural language processing (NLP) techniques, as well as for visualizing and editing representations of regulatory systems. These systems describe both signal transduction and biochemical pathways within complex multicellular organisms, yeast, and bacteria. This computer application in turn requires the development of a domain-specific ontology, or knowledge model. RESULTS: We introduce an ontological model for the representation of biological knowledge related to regulatory networks in vertebrates. We outline a taxonomy of the concepts, define their 'whole-to-part' relationships, describe the properties of major concepts, and outline a set of the most important axioms. The ontology is partially realized in a computer system designed to aid researchers in biology and medicine in visualizing and editing a representation of a signal transduction system.     

Using contextual and lexical features to restructure and validate the classification of biomedical concepts

Background  

Biomedical ontologies are critical for integration of data from diverse sources and for use by knowledge-based biomedical applications, especially natural language processing as well as associated mining and reasoning systems. The effectiveness of these systems is heavily dependent on the quality of the ontological terms and their classifications. To assist in developing and maintaining the ontologies objectively, we propose automatic approaches to classify and/or validate their semantic categories. In previous work, we developed an approach using contextual syntactic features obtained from a large domain corpus to reclassify and validate concepts of the Unified Medical Language System (UMLS), a comprehensive resource of biomedical terminology. In this paper, we introduce another classification approach based on words of the concept strings and compare it to the contextual syntactic approach.     

Ten Years of the Relative Risk Model and Regional Scale Ecological Risk Assessment

It has been 10 years since the publication of the relative risk model (RRM) for regional scale ecological risk assessment. The approach has since been used successfully for a variety of freshwater, marine, and terrestrial environments in North America, South America, and Australia. During this period the types of stressors have been expanded to include more than contaminants. Invasive species, habitat loss, stream alteration and blockage, temperature, change in land use, and climate have been incorporated into the assessments. Major developments in the RRM have included the extensive use of geographical information systems, uncertainty analysis using Monte Carlo techniques, and its application to retrospective assessments to determine causation. The future uses of the RRM include assessments for forestry and conservation management, an increasing use in invasive species evaluation, and in sustainability. Developments in risk communication, the use of Bayesian approaches, and in uncertainty analyses are on the horizon.     

Threshold-free high-power methods for the ontological analysis of genome-wide gene-expression studies

Ontological analysis facilitates the interpretation of microarray data. Here we describe new ontological analysis methods which, unlike existing approaches, are threshold-free and statistically powerful. We perform extensive evaluations and introduce a new concept, detection spectra, to characterize methods. We show that different ontological analysis methods exhibit distinct detection spectra, and that it is critical to account for this diversity. Our results argue strongly against the continued use of existing methods, and provide directions towards an enhanced approach.     

Use of a capacitive measuring mat for recording inter-fragment pressures and pressure distribution in ventral inter-corporal spondylodesis

With respect to ventral interbody fusion, rates of pseudarthrosis of up to 30% are reported. With the aim of reducing this figure, the use of dorsal fixation systems to stabilise the fused spinal units is recommended by a number of authors. The aim of these osteosynthetic procedures is to elevate the interfragmentary compression between the ventral bone block and the adjacent vertebrae. In order to measure the pressure achievable, and its local distribution, an experimental investigation involving the use of a capacitive measuring mat has been designed. The system of capacitive measurement and its application to the spine is described. The simple mode of measurement and mechanical stability, combined with high accuracy, are the specific advantages of capacitive systems of measurement. Especially in the documentation of interfragmentary pressure and pressure distribution, capacitive measuring mats are superior to comparable systems.     

Organic Codes: A Unifying Concept for Life

Although the knowledge about biological systems has advanced exponentially in recent decades, it is surprising to realize that the very definition of Life keeps presenting theoretical challenges. Even if several lines of reasoning seek to identify the essence of life phenomenon, most of these thoughts contain fundamental problem in their basic conceptual structure. Most concepts fail to identify either necessary or sufficient features to define life. Here, we analyzed the main conceptual frameworks regarding theoretical aspects that have been supporting the most accepted concepts of life, such as (i) the physical, (ii) the cellular and (iii) the molecular approaches. Based on an ontological analysis, we propose that Life should not be positioned under the ontological category of Matter. Yet, life should be better understood under the top-level ontology of “Process”. Exercising an epistemological approach, we propose that the essential characteristic that pervades each and every living being is the presence of organic codes. Therefore, we explore theories in biosemiotics and code biology in order to propose a clear concept of life as a macrocode composed by multiple inter-related coding layers. This way, as life is a sort of metaphysical process of encoding, the living beings became the molecular materialization of that process. From the proposed concept, we show that the evolutionary process is a fundamental characteristic for life’s maintenance but it is not necessary to define life, as many organisms are clearly alive but they do not participate in the evolutionary process (such as infertile hybrids). The current proposition opens a fertile field of debate in astrobiology, epistemology, biosemiotics, code biology and robotics.

     

Animal husbandry: the period 1973-1995

In the last decade the intensification of the pig and poultry industries has continued with increases in production unit size and in efficiency. This has come about as a response to rising costs, competition and reasonable end-product prices. The dairy industry has also expanded output through increasing milk yield per cow, encouraged by favourable market support. However, efficiency of feed conversion to milk production is still not directly selected for in dairy cattle. Developments in beef cattle have been away from intensive systems of production in an effort to reduce capital expenditure and increases in sheep productivity have been largely through increased stocking rates, greater fertilizer use and better grazing systems. In the next decade there are many feasible technological advances awaiting application. The use of computer simulation is likely to assist in predicting quantitative and qualitative body compositional responses to nutrition and in increasing the efficiency of grass utilization, while microprocessor technology will be developed into artificial aids to the stockman. Studies of reproductive physiology will continue to help increase output, especially with pigs and sheep. The building of sophisticated housing is likely to be justified for pigs, poultry, dairy cattle and calves, but not for suckler beef and sheep. There is likely to be greater use of centralized breeding schemes for dairy cattle, beef cattle and sheep. The future application of technology will be limited by a number of socio-economic factors. For example, the use of milk quotas to control surplus production will act as a powerful economic constraint to increased milk production and the growing public concern over animal welfare, pollution and health aspects of animal produce will exert increasing pressure on certain systems of production.     

Rehabilitating Reductionism

SYNOPSIS: Reductionism has become the object of a great dealof criticism from a variety of quarters within evolutionarybiology in recent years. Many contemporary anti-reductionistsargue that reductionism is inappropriate in biological inquirygiven the prevalence of hierarchies, scales of complexity andlevels of organization in the organic world. They further contendthat a commitment to reductionism has led evolutionary theoriststo make a large number of methodological blunders and conceptualerrors in constructing explanations of biological evolution. The contemporary critics of reductionism have not made a persuasivecase for the ontological peculiarity of the organic world. Muchof their argument concerning hierarchy and levels appears torest on assertion rather than metaphysical necessity or ontologicalpeculiarity. Moreover, the interpretations of reductionism attackedby contemporary critics in biology are narrow and overly simplistic. The modern synthetic theory of evolution may well have explanatoryinadequacies that demand the attention of biologists workingin many fields. But attempts to motivate theoretical alternativesto this theory based solely on ontological grounds appear toplace the ontological cart before the theoretical horse. Theoriesdictate ontological commitments and, as a result, it is at thelevel of theoretical rather than ontological adequacy that theassessment of the modern synthetic theory ought to proceed.