Scaling processes and problems

A personal view is presented of current approaches to scaling processes and variables in the context of better understanding ecosystem function and predicting the consequences of global environmental change. Issues considered include spatial and temporal scales of interest, the scaling process, scaling strategy, scaling problems, heterogeneity, patchiness and non-linearity, aggregation methodology and feedbacks. Knowledge of processes in plants and vegetation is largely at small scales. The transfer of this knowledge up to larger spatial and longer temporal scales is an open-ended process with potential errors arising from heterogeneity and patchiness in the distribution of processes and non-linearities in the functional relationships between processes and environmental variables. Scaling now covers several orders of magnitude with respect to spatial and temporal scales with attendant risks of propagating errors. At larger scales the wide diversity of vegetation classes poses a problem, and it is suggested that this can be countered by classifying classes of vegetation (not species) into a small number of ‘functional types’ of vegetation. Scaling through summation of component processes and through derivation of appropriately averaged parameters is considered. However, the increasing role of feedbacks at larger spatial and longer temporal scales is an essential feature of the scaling process. Thus, understanding the feedbacks and including them in upscaling schemes is a major priority. A scaling strategy is outlined to minimize the propagation of errors. Because the scaling process is open-ended it is essential that good models are used and tested at each increase in scale.     

Animal models and conserved processes

Background

The concept of conserved processes presents unique opportunities for using nonhuman animal models in biomedical research. However, the concept must be examined in the context that humans and nonhuman animals are evolved, complex, adaptive systems. Given that nonhuman animals are examples of living systems that are differently complex from humans, what does the existence of a conserved gene or process imply for inter-species extrapolation?

Methods

We surveyed the literature including philosophy of science, biological complexity, conserved processes, evolutionary biology, comparative medicine, anti-neoplastic agents, inhalational anesthetics, and drug development journals in order to determine the value of nonhuman animal models when studying conserved processes.

Results

Evolution through natural selection has employed components and processes both to produce the same outcomes among species but also to generate different functions and traits. Many genes and processes are conserved, but new combinations of these processes or different regulation of the genes involved in these processes have resulted in unique organisms. Further, there is a hierarchy of organization in complex living systems. At some levels, the components are simple systems that can be analyzed by mathematics or the physical sciences, while at other levels the system cannot be fully analyzed by reducing it to a physical system. The study of complex living systems must alternate between focusing on the parts and examining the intact whole organism while taking into account the connections between the two. Systems biology aims for this holism. We examined the actions of inhalational anesthetic agents and anti-neoplastic agents in order to address what the characteristics of complex living systems imply for inter-species extrapolation of traits and responses related to conserved processes.

Conclusion

We conclude that even the presence of conserved processes is insufficient for inter-species extrapolation when the trait or response being studied is located at higher levels of organization, is in a different module, or is influenced by other modules. However, when the examination of the conserved process occurs at the same level of organization or in the same module, and hence is subject to study solely by reductionism, then extrapolation is possible.     

Implicit and explicit processes in social cognition

In this review we consider research on social cognition in which implicit processes can be compared and contrasted with explicit, conscious processes. In each case, their function is distinct, sometimes complementary and sometimes oppositional. We argue that implicit processes in social interaction are automatic and are often opposed to conscious strategies. While we are aware of explicit processes in social interaction, we cannot always use them to override implicit processes. Many studies show that implicit processes facilitate the sharing of knowledge, feelings, and actions, and hence, perhaps surprisingly, serve altruism rather than selfishness. On the other hand, higher-level conscious processes are as likely to be selfish as prosocial.     

Lateralization of olfactory processes

Over the last ten years, methods of cerebral imaging have revolutionized our knowledge of cognitive processes in humans. An impressive number of papers dealing with cerebral imaging for olfaction have been published to date. Whereas the early works revealed those structures participating in the processing of odours presented passively to subjects, researchers later recorded brain activity when subjects performed specific olfactory tasks based on memory, emotion and identification. From these results, we suggest that there is a dissociation of olfactory processes, with involvement of the right hemisphere in memory processes and the left hemisphere in emotional processes. The review concludes with a summary of how these lateralized processes are consistent with the gestalt-nature of our olfactory perception.     

Membranes and membrane processes in biotechnology

Membrane and membrane processes are now receiving increasing attention as an efficient tool in modern biotechnology for downstream processing of bioreactor constituents, sterilization of feed streams or immobilization of biocatalysts. This paper reviews the major areas of application of membranes and membrane processes in biotechnology; problems relating to today's use of membranes and future developments are also discussed.     

Pre-enzymic origin of metabolic redox processes and of the energy storage processes

A treatment of the energetic conditions which regulate the non-equilibrium occurrence of metabolic redox processes associated with degradations of carbon chains or formations of condensed bonds shows that such processes are conditioned by the nature of the substrates and not by the preexistence of enzymic catalysts or cellular ultrastructures. An experimental program has been initiated to spectrophotometrically, electrochemically and chemically detect which redox components appear during model, studies of chemical evolution, operating from simple mixtures of CH₄, NH₃, H₂ and water and from the same mixtures with added phosphorus or sulfur derivatives and metal cations.     

Developmental processes and the evolution of plant clonality

A common type of clonal plant grows limited ramets that are connected by modified stems. Three major developmental processes are required for this clonality: the differentiation of specialized plagiotropic stems which act as spacers, the localized formation of adventitious roots, and a limitation of vertical development which is coupled with repeated rejuvenation. Intermediate forms, in which one of these processes occurs without the others, are readily found. Studies of apical initiation and differentiation in a-clonal plants suggest mechanisms for these processes, based on modified hormonal correlations and maturation processes within apices. The consideration of developmental processes, which has been relatively neglected, can therefore be a key to understanding the possibilities and limitations of clonal evolution. For example, comparative developmental studies point to convergent or parallel evolution, in which a similar outcome has been based on different developmental mechanisms. A consideration of developmental processes also throws new light on clonal organization and raises concrete questions that are amenable to experimental work.     

Optimizing scale-up fermentation processes

There are many aims associated with the optimization of fermentation processes. Optimization is expected to increase the yield of the final product but the process must be compliant with good manufacturing practices, the available equipment and the expected final scale of operation. Dealing with genetically modified microorganisms that overproduce recombinant protein has the advantage that the vast majority of the processes use only three different species, namely Escherichia coli, Saccharomyces cerevisiae and Pichia pastoris. Standard processes for each organism are described in textbooks and serve as a basis for the development of a tailored process. This article outlines the general philosophy that we have devised to ensure an efficient approach of scaling up fermentation processes for biopharmaceutical purposes, in a multidisciplinary environment.     

Redox processes in biological systems

General principles of organization and distinctive features of the redox processes of biological systems are discussed. We paid special attention to the most examined parts of redox biology. As one of the approaches to the generalization of accumulated knowledge about redox processes, the so-called redox hypothesis of oxidative stress was examined. Extrapolation of this hypothesis on the processes taking place in plant cells, formulated on the basis of thiol-disulfide metabolism of animal cells, may help to systematize the available knowledge about redox processes in plants.     

Low-level and high-level processes in apparent motion

When a group of dots within a random-dot array is discontinuously displaced, it appears as a moving region perceptually segregated from its stationary surround. The spastial, temporal and other constraints governing this effect are markedly different from those classically found for the apparent motion of isolated stimulus elements. The random-dot display appears to tap a low-level motion-detecting process, distinct from the more interpretive process elicited by the classical displays. The distinct contributions of these processes can be identified in 'multi-stable' displays which yield alternative percepts of apparent motion depending on which one or both of the processes is activated. Such experiments illustrate the interaction of relatively stimulus-constrained and relatively autonomous processes invisual perception.     

Polynucleotide evolution and branching processes

The theory of multitype branching processes is applied to the kinetics of polynucleotide replication. The results obtained are compared with the solutions of the deterministic differential equations of conventional chemical kinetics.     

Functional equivalence of industrial metal cleaning processes comparison of metal cleaning processes within LCA

In an LCA case study, the three most frequent industrial metal cleaning technologies were assessed: Cleaning based on aqueous cleaning agents, non-halogenated hydrocarbon solvents and halogenated hydrocarbon solvents. Beside optimisation analysis, the comparison of the cleaning processes was a main goal of the study. The function of metal cleaning processes can be described with a set of parameters called functional parameters. In order to compare different cleaning processes within LCA, it is a precondition that all relevant functional parameters be equivalent. However, metal cleaning processes from different companies normally differ in most of the functional parameters and, thus, are not functionally equivalent. Therefore, it is necessary to calculate the material and energy flows of the processes corresponding to a reference function as a basis for comparison. This can be achieved by simulating the processes according to the functional parameters with the help of a process model. For a general comparison of the technologies, it is also necessary to consider the assessed machines having the same level of optimisation and the same scale.     

Developmental processes regulate craniofacial variation in disease and evolution

Variation in development mediates phenotypic differences observed in evolution and disease. Although the mechanisms underlying phenotypic variation are still largely unknown, recent research suggests that variation in developmental processes may play a key role. Developmental processes mediate genotype–phenotype relationships and consequently play an important role regulating phenotypes. In this review, we provide an example of how shared and interacting developmental processes may explain convergence of phenotypes in spliceosomopathies and ribosomopathies. These data also suggest a shared pathway to disease treatment. We then discuss three major mechanisms that contribute to variation in developmental processes: genetic background (gene–gene interactions), gene–environment interactions, and developmental stochasticity. Finally, we comment on evolutionary alterations to developmental processes, and the evolution of disease buffering mechanisms.     

Photochemical processes and the environmental impact of petroleum spills

A review of the photochemical processes involved in the degradation of petroleum,its products, and some model compounds found in petroleum. Emphasis is given to processes which affect emulsification, water solubility, and toxicity. Waterphase photodegradation is also treated. The interaction of these processes withbiodegradation is discussed. Areas requiring further work are indicated. 96references.     

Modelling biological processes using workflow and Petri Net models

MOTIVATION: Biological processes can be considered at many levels of detail, ranging from atomic mechanism to general processes such as cell division, cell adhesion or cell invasion. The experimental study of protein function and gene regulation typically provides information at many levels. The representation of hierarchical process knowledge in biology is therefore a major challenge for bioinformatics. To represent high-level processes in the context of their component functions, we have developed a graphical knowledge model for biological processes that supports methods for qualitative reasoning. RESULTS: We assessed eleven diverse models that were developed in the fields of software engineering, business, and biology, to evaluate their suitability for representing and simulating biological processes. Based on this assessment, we combined the best aspects of two models: Workflow/Petri Net and a biological concept model. The Workflow model can represent nesting and ordering of processes, the structural components that participate in the processes, and the roles that they play. It also maps to Petri Nets, which allow verification of formal properties and qualitative simulation. The biological concept model, TAMBIS, provides a framework for describing biological entities that can be mapped to the workflow model. We tested our model by representing malaria parasites invading host erythrocytes, and composed queries, in five general classes, to discover relationships among processes and structural components. We used reachability analysis to answer queries about the dynamic aspects of the model. AVAILABILITY: The model is available at http://smi.stanford.edu/projects/helix/pubs/process-model/.     

Novel microbial nitrogen removal processes

The present-day wastewater treatment practices can be significantly improved through the introduction of new microbial treatment technologies. Recently, several new processes for nitrogen removal have been developed. These new nitrogen removal technologies provide practicable options for treating nitrogen-laden wastewaters. The new processes are based on partial nitrification of ammonium to nitrite combined with anaerobic ammonium oxidation. These processes include the single reactor system for high ammonia removal over nitrite (SHARON) process, which involves part conversion of ammonium to nitrite; the anaerobic ammonium oxidation (ANAMMOX) process, which involves anaerobic ammonium oxidation; and the completely autographic nitrogen removal over nitrite (CANON) process, which involves nitrogen removal within one reactor under oxygen-limited conditions. These new processes target the removal of nitrogen from wastewaters containing significant quantities of ammonium.     

Marcov processes and neuronal engram formation--a model]

The multivariate partial autocorrelation bases on the noncircular serial correlation matrices and is a problem of eigen values. Autoregressive oscillations of a time series and its order can be tested. MARCOV processes are 1st order processes, they are found during the conversion of short into long time memory (conditioned avoidance response).     

Mutated genes,pathways and processes in tumours

Integration of the many available sources of cancer gene information—such as large‐scale tumour‐resequencing studies— identifies the ‘usual suspect’ genes, mutated in many tumour types, as well as different sets of mutated genes according to the specific tumour type. Scaling‐up the analysis reveals that this large collection of mutated genes cluster into a smaller number of signalling pathways and processes. From this, we draw a map of the altered processes, and their combinations, in more than 10 tumours types. Literature searches identify pathways and processes that are covered sparsely in the literature, and invite the proposal of new hypotheses to investigate cancer initiation and progression.     

Models of Darwinian processes and evolutionary principles

Evolutionary processes are described as stochastic motions in a genotype space (set of sequences with a Hamming distance) and a phenotype space (vector space of phenotypic properties). Real value functions are introduced which form a landscape over these spaces; smoothness postulates are formulated. Evolution is considered as a kind of hill climbing on these adaptive landscapes. A rather simple diffusion approximation for the phenotypic processes is proposed which leads to similar mathematical problems as the Schrödinger equation for disordered potential distributions.     

Recycle in fermentation processes

Until recently, the recycle of the solid (microbial), liquid, or gaseous phases in microbiological processes has only been practiced rarely, with the notable exception of activated sludge processes for wastewater treatment, where recycling of a large fraction of the microbial phase is essential for process stability and performance. During the last decade, the economic impact of a number of politically motivated changes with respect to energy and feedstock costs and availability, and legislation directed towards markedly higher levels of environmental protection have encouraged the evaluation and subsequent development of recycle technology in the fermentation industry. Many of the developments have occurred in isolation and some have failed to result in either an improvement in process economics or any reduction in the quantity of pollutants discharged. This article seeks to review the present diversity of approaches to recycle technology in fermentation processes in order to provide a sensible basis for future developments.