Modes of speciation and the neutral theory of biodiversity

Hubbell's neutral theory of biodiversity has generated much debate over the need for niches to explain biodiversity patterns. Discussion of the theory has focused on its neutrality assumption, i.e. the functional equivalence of species in competition and dispersal. Almost no attention has been paid to another critical aspect of the theory, the assumptions on the nature of the speciation process. In the standard version of the neutral theory each individual has a fixed probability to speciate. Hence, the speciation rate of a species is directly proportional to its abundance in the metacommunity. We argue that this assumption is not realistic for most speciation modes because speciation is an emergent property of complex processes at larger spatial and temporal scales and, consequently, speciation rate can either increase or decrease with abundance. Accordingly, the assumption that speciation rate is independent of abundance (each species has a fixed probability to speciate) is a more natural starting point in a neutral theory of biodiversity. Here we present a neutral model based on this assumption and we confront this new model to 20 large data sets of tree communities, expecting the new model to fit the data better than Hubbell's original model. We find, however, that the data sets are much better fitted by Hubbell's original model. This implies that species abundance data can discriminate between different modes of speciation, or, stated otherwise, that the mode of speciation has a large impact on the species abundance distribution. Our model analysis points out new ways to study how biodiversity patterns are shaped by the interplay between evolutionary processes (speciation, extinction) and ecological processes (competition, dispersal).     

Être-au-monde et être cosmique

What are the relationships between our immediate, experiential (phenomenological) understanding of the surrounding objects and the scientific understanding presently available on these phenomena? This should be one of the most important issues for contemporary philosophy. The problematic link between these two ways of knowing is illustrated in the text by the experience of contemplating the starry sky. The contemporary astrophysical knowledge has emphasised the incommensurability between the spatial and temporal scale of cosmic events and that of our experience in which, however, the universe is understood. That leads us to acknowledge the interdependency of the two issues, of the cosmic being and of the being-to-the-world, which deserves to be studied following the works of Simondon, and on which can be grounded an ethics, allowing a form of philosophical serenity.     

Synthetic biology and the technicity of biofuels

The principal existing real-world application of synthetic biology is biofuels. Several ‘next generation biofuel’ companies—Synthetic Genomics, Amyris and Joule Unlimited Technologies—claim to be using synthetic biology to make biofuels. The irony of this is that highly advanced science and engineering serves the very mundane and familiar realm of transport. Despite their rather prosaic nature, biofuels could offer an interesting way to highlight the novelty of synthetic biology from several angles at once. Drawing on the French philosopher of technology and biology Gilbert Simondon, we can understand biofuels as technical objects whose genesis involves processes of concretisation that negotiate between heterogeneous geographical, biological, technical, scientific and commercial realities. Simondon’s notion of technicity, the degree of concretisation of a technical object, usefully conceptualises this relationality. Viewed in terms of technicity, we might understand better how technical entities, elements, and ensembles are coming into being in the name of synthetic biology. The broader argument here is that when we seek to identify the newness of disciplines, their newness might be less epistemic and more logistic.     

What is an organism? An immunological answer

The question, "What is an organism?," formerly considered as essential in biology, has now been increasingly replaced by a larger question, "What is a biological individual?" On the grounds that i) individuation is theory-dependent, and ii) physiology does not offer a theory, biologists and philosophers of biology have claimed that it is the theory of evolution by natural selection that tells us what counts as a biological individual. Here I show that one physiological field, immunology, offers a theory that makes possible a biological individuation based on physiological grounds. I give a new answer to the question of the individuation of an organism by linking together the evolutionary and the immunological approaches to biological individuation.     

Developing unified theories in ecology as exemplified with diversity gradients

A scientific field matures as its theoretical underpinnings consolidate around unified theories: conceptual structures consisting of a few general propositions that encompass a wide domain of phenomena and from which can be derived an array of models. We demonstrate this process with a synthetic theory of ecological gradients and species richness. Our unified theory rests on four propositions. First, variation in some environmental factor effects variation in the number of individuals creating a gradient. Second, in a uniform environment of fixed area, more individuals lead to more species. Third, the variance of an environmental factor increases with its mean for sites of equal area. Fourth, all nonmonotonic relationships (i.e., hump shaped or U shaped) require a trade-off in organismal performance or in population characteristics with respect to the environmental gradient. We identify 17 models that link environmental gradients with diversity, show their relationship to our framework, and describe issues surrounding their empirical testing. We illustrate how a general theory can be used to build new models such as that for the U-shaped productivity-diversity relationship. Finally, we discuss how our theory could be unified further with other theories of diversity and indicate other areas of ecology that are ripe for unification. By providing an example of the process of theory unification, we hope to encourage such efforts throughout ecology.     

Hylomorphism and the Metabolic Closure Conception of Life

This paper examines three exemplary theories of living organization with respect to their common feature of defining life in terms of metabolic closure: autopoiesis, (M, R) systems, and chemoton theory. Metabolic closure is broadly understood to denote the property of organized chemical systems that each component necessary for the maintenance of the system is produced from within the system itself, except for an input of energy. It is argued that two of the theories considered—autopoiesis and (M, R) systems—participate in a hylomorphist pattern of thinking which separates the “form” of the living system from its “matter.” The analysis and critique of hylomorphism found in the work of the philosopher Gilbert Simondon is then applied to these two theories, and on the basis of this critique it is argued that the chemoton model offers a superior theory of minimal life which overcomes many of the problems associated with the other two. Throughout, the relationship between hylomorphism and the understanding of living things as machines is explored. The paper concludes by considering how hylomorphism as a background ontology for theories of life fundamentally influences the way life is defined.     

Individuation in Sorghum bicolor: a self-organized process involved in physiological adaptation to salinity

In Sorghum bicolor, salt-adaptation was defined as the capacity of plants to grow at 300 m M NaCl (a lethal concentration) following a 3-week pre-treatment with 150 m M NaCl (a sublethal concentration). Large populations induced for salt-adaptation were analysed. Two modes of osmotic regulation (Na-includer and Na-excluder) were differentiated during induction of salt-adaptation, in spite of the genetic and environmental homogeneity. This variability was not related to any incapacity of the Na-includers to control accumulation of Na ⁺ ions in the shoot, because most of the pre-treated plants displayed a similar capacity of growth and control of Na ⁺ uptake after transfer to 300 m M NaCl. This unsuspected complexity of initially homogeneous populations points on the inadequacy of physiological studies focused on the ‘average individual’. Further analyses showed that variability was not directly related to micro-environmental variations. It is concluded that a process of individuation is caused by a third source of variability, which is the expression of a self-organizing process normally occurring during the transition phases in development. In constraining environments, this phenomenon of individuation includes adaptive modifications.     

A structured hazard identification method of human error for shale gas fracturing operation

Shale gas fracturing is a complex system of continuous operation. If human errors occur, it will cause a chain reaction, from abnormal events to fracturing accidents, and even lead to abandonment of shale gas wells. The process of shale gas fracturing has many production stages that are complex and the consequence of any error is serious. The human error modes in shale gas fracturing process are mutative. Therefore, human error should be studied in a systematic way, and in a hybrid framework, that is, whole integration of identification, prioritization, reasoning, and control. A new structured identification method of human error in a hybrid framework for shale gas fracturing operation is presented in the article. First, human error is structurally identified based on the human HAZOP method. Second, fuzzy VIKOR method is applied to comprehensive prioritization. Finally, 4M element theory is used to analyze the human error and control its evolution. The method improves the consistency of the identification results through the standard identification step and the identification criterion. Results from a study of feed-flow process indicate that 34 kinds of human errors can be identified, and high-probability errors occur in the behavior of implementation and observation.     

Scalable Session Locking for a Distributed File System

File systems provide an interface for applications to obtain exclusive access to files, in which a process holds privileges to a file that cannot be preempted and restrict the capabilities of other processes. Local file systems do this by maintaining information about the privileges of current file sessions, and checking subsequent sessions for compatibility. Implementing exclusive access in this manner for distributed file systems degrades performance by requiring every new file session to be registered with a lock server that maintains global session state. We present two techniques for improving the performance of session management in the distributed environment. We introduce a distributed lock for managing file access, called a semi-preemptible lock, that allows clients to cache privileges. Under a semi-preemptible lock, a file system creates new sessions without messages to the lock manager. This improves performance by exploiting locality – the affinity of files to clients. We also present data structures and algorithms for the dynamic evaluation of locks that allow a distributed file system to efficiently manage arbitrarily complex locking. In this case, complex means that an object can be locked in a large number of unique modes. The combination of these techniques results in a distributed locking scheme that supports fine-grained concurrency control with low memory and message overhead and with the assurance that their locking system is correct and avoids unnecessary deadlocks.     

Concepts of an architectonic approach to transformation morphology

This paper is about a general methodology for pattern transformation. Patterns are network representations of the relations among structures and functions within an organism. Transformation refers to any realistic or abstract transformation relevant to biology, e.g. ontogeny, evolution and phenotypic clines. The main aim of the paper is a methodology for analyzing the range of effects on a pattern due to perturbing one or more of its structures and/or functions (transformation morphology). Concepts relevant to such an analysis of pattern transformation are reviewed and several new ones introduced: pattern unit; direct and indirect functional demands; compatibility and trade-off; integrating, adding and decoupling; functional effectiveness; spatial, profile and other architectonic constraints; domains of structure-function relations; goal and process adaptability; multiple pathways. The paper is written from the the perspective of architectonic morphology, viz. functional morphology focusing on the relation between anatomical coherence and the compatibility of functions. The advantages and disadvantages of inductive and deductive approaches are discussed.     

Genome editing: intellectual property and product development in plant biotechnology

Genome editing is a revolutionary technology in molecular biology. While scientists are fascinated with the unlimited possibilities provided by directed and controlled changes in DNA in eukaryotes and have eagerly adopted such tools for their own experiments, an understanding of the intellectual property (IP) implications involved in bringing genome editing-derived products to market is often lacking. Due to the ingenuity of genome editing, the time between new product conception and its actual existence can be relatively short; therefore knowledge about IP of the various genome editing methods is relevant. This point must be regarded in a national framework as patents are instituted nationally. Therefore, when designing scientific work that could lead to a product, it is worthwhile to consider the different methods used for genome editing not only for their scientific merits but also for their compatibility with a speedy and reliable launch into the desired market.     

Exploring the evolution of Wolbachia compatibility types: a simulation approach

Wolbachia-induced cytoplasmic incompatibility (CI) is observed when males bearing the bacterium mate with uninfected females or with females bearing a different Wolbachia variant; in such crosses, paternal chromosomes are lost at the first embryonic mitosis, most often resulting in developmental arrest. The molecular basis of CI is currently unknown, but it is useful to distinguish conceptually the male and female sides of this phenomenon: in males, Wolbachia must do something, before it is shed from maturing sperm, that will disrupt paternal chromosomes functionality [this is usually termed "the modification (mod) function"]; in females, Wolbachia must somehow restore embryonic viability, through what is usually called "the rescue (resc) function." The occurrence of CI in crosses between males and females bearing different Wolbachia variants demonstrates that the mod and resc functions interact in a specific manner: different mod resc pairs make different compatibility types. We are interested in the evolutionary process allowing the diversification of compatibility types. In an earlier model, based on the main assumption that the mod and resc functions can mutate independently, we have shown that compatibility types can evolve through a two-step process, the first involving drift on mod variations and the second involving selection on resc variations. This previous study has highlighted the need for simulation-based models that would include the effects of nondeterministic evolutionary forces. This study is based on a simulation program fulfilling this condition, allowing us to follow the evolution of compatibility types under mutation, drift, and selection. Most importantly, simulations suggest that in the frame of our model, the evolution of compatibility types is likely to be a gradual process, with new compatibility types remaining partially compatible with ancestral ones.     

Offshore port service concepts: classification and economic feasibility

Most prevalent among the approaches to address the ever increasing demands for port capacity are the construction of new berths, installation of faster cranes and optimization of existing resources. A less common approach is to employ offshore port service concepts. Here, we endeavor to provide a complete survey of such nontraditional offshore service concepts and demonstrate that all, except a few very unusual concepts, can be well classified into one of thirty two structures or their combinations. Advantages, disadvantages and the container handling chain are discussed. We identify which of these structures can provide any of six possible operational modes. We next focus on a subset of the thirty two structures called the mobile harbor. This concept has recently been proposed and shares some similarities with midstream operation in Hong Kong. We endeavor to address the fundamental question: “Should such a concept be implemented?” We develop an estimate of the cost per unit threshold below which this concept will be viable. The per unit cost estimate of current MH designs is within about 6% of the economic viability threshold for traditional operation in Hong Kong. Other operational modes are not as favorable. As our focus is on the feasibility of the operational paradigm, we do not here address technology issues except to note ongoing efforts to resolve technology hurdles.     

Aspartic protease inhibitors. An integrated approach for the design andsynthesis of diaminodiol-based peptidomimetics.

Aspartic proteases play key roles in a variety of pathologies, including acquired immunodeficiency syndrome. Peptidomimetic inhibitors can act as drugs to combat these pathologies. We have developed an integrated methodology for preparing human immunodeficiency virus (HIV)-1 aspartic protease diaminodiol inhibitors, based on a computational method that predicts the potential inhibitory activity of the designed structures in terms of calculated enzyme-inhibitor complexation energies. This is combined with a versatile synthetic strategy that couples a high degree of stereochemical control in the central diaminodiol module with complete flexibility in the choice of side chains in the core and in flanking residues. A series of 23 tetrameric, pentameric and hexameric inhibitors, with a wide range of calculated relative complexation energies (-47.2 to +117 kJ.mol-1) and predicted hydrophobicities (logPo/w = 1.8-8.4) was thus assembled from readily available amino acids and carboxylic acids. The IC50 values for these compounds ranged from 3.2 nM to 90 microM, allowing study of correlations between structure and activity, and individuation of factors other than calculated complexation energies that determine the inhibition potency. Multivariable regression analysis revealed the importance of side-chain bulkiness and rigidity at the P2, P2' positions, suggesting possible improvements for the prediction process used to select candidate structures.     

Alternative models for the evolution of eyespots and of serial homology on lepidopteran wings

Serial homology is widespread in organismal design, but the origin and individuation of these repeated structures appears to differ with the different types of serial homologues, and remains an intriguing and exciting topic of research. Here I focus on the evolution of the serially repeated eyespots that decorate the margin of the wings of nymphalid butterflies. In this system, unresolved questions relate to the evolutionary steps that lead to the appearance of these serial homologues and how their separate identities evolved. I present and discuss two alternative hypotheses. The first proposes that eyespots first appeared as a row of undifferentiated repeated modules, one per wing compartment, that later become individuated. This individuation allowed eyespots to appear and disappear from specific wing compartments and also allowed eyespots to acquire different morphologies. The second hypothesis proposes that eyespots first appeared as individuated single units, or groups of units, that over evolutionary time were co-opted into new compartments on the wing. I discuss the merits of each of these alternate hypotheses by finding analogies to other systems and propose research avenues for addressing these issues in the future.     

Biotechnology to improve health in developing countries -- a review

The growing health disparities between the developing and the developed world call for urgent action from the scientific community. Science and technology have in the past played a vital role in improving public health. Today, with the tremendous potential of genomics and other advances in the life sciences, the contribution of science to improve public health and reduce global health disparities is more pertinent than ever before. Yet the benefits of modern medicine still have not reached millions of people in developing countries. It is crucial to recognize that science and technology can be used very effectively in partnership with public health practices in developing countries and can enhance their efficacy. The fight to improve global health needs, in addition to effective public health measures, requires rapid and efficient diagnostic tools; new vaccines and drugs, efficient delivery methods and novel approaches to therapeutics; and low-cost restoration of water, soil and other natural resources. In 2002, the University of Toronto published a report on the "Top 10 Biotechnologies for Improving Health in Developing Countries". Here we review these new and emerging biotechnologies and explore how they can be used to support the goals of developing countries in improving health.