Phenomenon of Life: Between Equilibrium and Non-Linearity

A model of ordering applicable to biological evolution is presented. It is shown that a steady state (more precisely approaching to a steady state) system of irreversible processes, under conditions of disproportionation of entropy, produces a lower-entropy product, that is, ordering. The ordering is defined as restricting of degrees of freedom: freedom of motion, interactions etc. The model differs from previous ones in that it relates the ordering to processes running not far from equilibrium, described in the linear field of non-equilibrium thermodynamics. It is shown that a system, which includes adenosine triphosphate (ATP) to adenosine diphosphate (ADP) conversion meets the demands of the physical model: it provides energy maintaining steady state conditions, and hydrolysis of ATP proceeding with consumption of water can be tightly conjugated with the most important reactions of synthesis of organic polymers (peptides, nucleotide chains etc.), which proceed with release of water. For these and other reasons ATP seems to be a key molecule of prebiotic evolution. It is argued that the elementary chemical reaction proceeding under control of an enzyme is not necessarily far from equilibrium. The experimental evidence supporting this idea, is presented. It is based on isotope data. Carbon isotope distribution in biochemical systems reveals regularity, which is inherent to steady state systems of chemical reactions, proceeding not far from equilibrium. In living organisms this feature appears at the statistical level, as many completely irreversible and non-linear processes occur in organisms. However not-far-from-equilibrium reactions are inherent to biochemical systems as a matter of principle. They are reconcilable with biochemical behavior. Extant organisms are highly evolved entities which, however, show in their basis the same features, as the simplest chemical systems must have had been involved in the origin of life. Some consequences following from the model, which may be significant for understanding the origin of life and the mechanism of biological evolution, are pointed out.     

The detection of salivary enzymes of phytophagous Hemiptera: a compilation of methods

The role of Hemipteran saliva and salivary enzymes is central to an understanding of the etiology of damage that these insects cause to plants. The dilute nature of the salivary secretions and the minute quantities in which they are often obtainable have made analysis and detection of salivary components very difficult. Such investigations in this laboratory have led us to formalise the techniques involved and we believe that the compilation of these methods presented herein may be useful to other research workers in this area. Methods are described for acid and alkaline phosphatase, esterase, /S-glucosidase, carbohydrases, invertase, amylase, proteinase, pectinase, cellulase, catalase, peroxidase, catechol oxidase, superoxide dismutase and ascorbic oxidase.     

Introduction: Understanding change through the analysis of continuity

This short text presents the third part of the volume. The five contributions illustrate the different levels at which reproduction can be considered-the individual, the family, the community, the population-but also their necessary interactions. The individual behaviour cannot but be understood in the context of his(her) family and community; the population dynamics is but the result of the family life cycle and the processes which took place within the community. The problem is therefore to choose the entity pertinent to each inquiry. Multilevel analysis make obvious the complexity of the notion of reproduction and of population dynamics. Translation from the french by Derek F. Roberts     

Biomphalaria glabrata amoebocytes: Assay of factors influencing in vitro phagocytosis

A simple and short-term in vitro assay system has been adapted for quantitative evaluation of the rate of phagocytosis of amoebocytes obtained from hemolymph of the pulmonate gastropod Biomphalaria glabrata. The variation in the rate of phagocytosis exhibited by amoebocyte monolayers prepared from individual snails is reduced by utilizing amoebocytes from pooled hemolymph from snails of similar sizes. The study demonstrates that the rate of phagocytosis depends on incubation time, temperature, and pH. Substantial inhibition of phagocytosis is exerted by 2-deoxy-d-glucose and 2-iodoacetamide but not by potassium cyanide, indicating that energy consumed during phagocytosis is generated by the glycolysis pathway.     

Motor activity of infusoria: Theoretical and applied aspects

The article considers morpho-functional organization of cilia—the infusorian locomotion organs—and shows a great complexity of motor behavior of these unicellulars. The problem of control of locomotor activity of infusorian as the single organism is discussed, and the conclusion is made that the system of control of movements is to be multilevel and to include receptor, afferent, central, efferent, and effector links. The role of central integrator and coordinator of motor behavior can be played by the cell nucleus (macronucleus) closely connected with periphery by cytoskeleton dynamic elements. The problem of fight with infusoria parasitizing in the human and animal bodies by impairing motor activity of these unicellulars is also discussed.     

Primeval cells: Possible energy-generating and cell-division mechanisms

Summary It is proposed that the first entity capable of adaptive Darwinian evolution consisted of a liposome vesicle formed of (1) abiotically produced phospholipidlike molecules; (2) a very few informational macromolecules; and (3) some abiogenic, lipid-soluble, organic molecule serving as a symporter for phosphate and protons and as a means of high-energy-bond generation. The genetic material had functions that led to the production of phospholipidlike materials (leading to growth and division of the primitive cells) and of the carrier needed for energy transduction. It is suggested that the most primitive exploitable energy source was the donation of 2H⁺+2e^– at the external face of the primitive cell. The electrons were transferred (by metal impurities) to internal sinks of organic material, thus creating, via a deficit, a protonmotive force that could drive both the active transport of phosphate and high-energy-bond formation.This model implies that proton translocation in a closed-membrane system preceded photochemical or electron transport mechanisms and that chemically transferable metabolic energy was needed at a much earlier stage in the development of life than has usually been assumed. It provides a plausible mechanism whereby cell division of the earliest protocells could have been a spontaneous process powered by the internal development of phospholipids. The stimulus for developing this evolutionary sequence was the realization that cellular life was essential if Darwinian survival of the fittest was to direct evolution toward adaptation to the external environment.     

Differentiation antigens of hemoblastoses and epithelial tumors: Relations to the mechanisms of transformation and progression

The role of mechanisms underlying differentiation is considered in malignant transformation of hemoblastoses and epithelial tumors. In hemoblastoses, differentiation is intimately related to malignant transformation and they are underlain by the same mechanisms. Immunophenotyping of hemoblastoses is fully based on successive stages of their differentiation with characteristic expression of differentiation antigens. Unlike hemoblastoses, epithelial tumors gradually, in the course of progression, lose their differentiation due to the degradation of the connections with the microenvironment, which controls the direction and level of epithelial differentiation. Therefore, carcinomas are characterized by varying degrees of “antigenic simplification”, including the epithelial-mesenchymal transition.     

Dielectrophoretic separation of cells: Continuous separation

Dielectrophoresis is the movement of particles in non-uniform alternating and direct current (AC, DC) electric fields. When nonuniform electric fields are created between microelectrodes, cells will redistribute themselves around the electrodes, the force holding the cells in place dependig on the local electric field and on the electrical properties of the cells themselves and the suspending medium. Steric drag forces produced by a gentle fluid flow in the chamber can be used to separate cells by selectively lifting cells from potential energy wells produced by the electric field. The technique is demonstrated in the batch separation of bacteria, yeast cells, and plant cells. Continuous separation and extraction of two cell types can be achieved by repeated reversing of the fluid flow direction in phase with the switching on and off of the applied voltage, and the efficacy of the technique is demonstrated for viable and nonviable (heat-treated) yeast cells. (c) 1995 John Wiley & Sons, Inc.     

Strategy for Stabilizing Enzymes Part Two: Increasing Enzyme Stability by Selective Chemical Modification

The molecular mechanisms of change in the thermal stability of proteins modified with low molecular weight reagents are discussed. The choice of stabilization mechanisms to be used as a general strategy for increasing enzyme stability by chemical modification is addressed. Hydrophilization of nonpolar surface areas is the most simple and reliable approach to artificial stabilization of enzymes for use in applied biochemistry and biotechnology.     

The Professionalization of Science Studies: Cutting Some Slack

During the past hundred years or so, those scholars studying science have isolated themselves as much as possible from scientists as well as from workers in other disciplines who study science. The result of this effort is history of science, philosophy of science and sociology of science as separate disciplines. I argue in this paper that now is the time for these disciplinary boundaries to be lowered or at least made more permeable so that a unified discipline of Science Studies might emerge. I discuss representative problems that stand in the way of such an integration. These problems may seem so formidable in the abstract that no one in their right mind would waste their time trying to bring about a unified field of Science Studies. However, those of us who limit ourselves to the study of the biological sciences have already formed a society in which workers from all disciplines can share their expertise -- the International Society for the History, Philosophy and Social Studies of Science.     

Evolutionary morphology of whip spiders: towards a phylogenetic system (Chelicerata: Arachnida: Amblypygi)*

The aim of this study is to present a cladogram and phylogenetic system and to use this to discuss the phylogeny and biogeography of the Amblypygi. A total of 29 morphological structures were studied, their plesiomorphic and apomorphic characters or character states were identified, and the resulting data matrix was analysed. As a result, the ‘old’Charontidae or Pulvillata emerge as a paraphyletic group; the genus Paracharon is the sister group of all other amblypygids, which are now termed Euamblypygi. The ‘new’Charontidae (sensu Quintero: the genera Stygophrynus and Charon) are the sister group of the Phrynida or Apulvillata; together they form the Neoamblypygi. The relationships of the genera of the Charinidae cannot be resolved with the available data. They may be a paraphyletic group. The genus Catageus is a possible candidate for being the sister group of the Neoamblypygi. The new system allows a discussion of the phylogeny and biogeography of whip spiders. It also points to unresolved taxa and thus indicates the questions future research should address.     

Bacterial clogging of porous media: A new modelling approach

A comparison is made between existing mathematical models and experimental data that relate the reduction of the saturated hydraulic conductivity (K) of a porous medium to the porosity reduction caused by microbial growth. The models yielded a realistic prediction of a data set obtained with a model porous medium consisting of millimeter‐size glass spheres, but failed to predict the clogging behaviour observed in smaller‐than‐1‐mm sand. A new modelling approach, semi‐mechanistic in nature, is proposed that gives good predictions of fine sand media as well. It relaxes the assumption about uniformly‐thick biofilms by allowing a second arrangement to occur, i.e. discrete plugs filling the pore lumen. The new model requires input data on two intrinsic properties of the system, which renders it sufficiently flexible as to fit very different data sets. The two model parameters are K_min, the minimum K value when all porosity is filled with microorganisms, and B_c, the biovolume fraction at which most cell detachment from biofilm occurs.     

Nano-intentionality: a defense of intrinsic intentionality

I suggest that most discussions of intentional systems have overlooked an important aspect of living organisms: the intrinsic goal-directedness inherent in the behaviour of living eukaryotic cells. This goal directedness is nicely displayed by a normal cell’s ability to rearrange its own local material structure in response to damage, nutrient distribution or other aspects of its individual experience. While at a vastly simpler level than intentionality at the human cognitive level, I propose that this basic capacity of living things provides a necessary building block for cognition and high-order intentionality, because the neurons that make up vertebrate brains, like most cells in our body, embody such capacities. I provisionally dub the capacities in question “nano-intentionality”: a microscopic form of “aboutness”. The form of intrinsic intentionality I propose is thoroughly materialistic, fully compatible with known biological facts, and derived non-mysteriously through evolution. Crucially, these capacities are not shared by any existing computers or computer components, and thus provide a clear, empirically-based distinction between brains and currently existing artificial information processing systems. I suggest that an appreciation of this aspect of living matter provides a potential route out of what may otherwise appear to be a hopeless philosophical quagmire confronting information-processing models of the mind.

Focus: Bioethics: The Emotions in Bioethical Decision-making

In an era of evidence-based medicine and an increasing use of technology the question is raised again as to what extent emotions should play in medical and ethical decision-making. While clearly the correct facts in each case are a sine qua non for ethical decision-making, and one should evaluate each situation rationally in accord with accepted ethical principles, the appropriate role of the emotions in decision-making is gaining increased attention in part as a result of newer research in neuroethics. In end-of-life care there often exists a disconnect between the “rational” analysis by many philosophers and ethicists and the emotional reactions of many physicians and nurses with respect to the comparison between withholding and withdrawal of life-sustaining therapy. It is suggested that these attitudes of many health care workers should not be ignored because they represent a critical, almost universal, and laudable value of reluctance to take human life, a value so strongly ingrained in the ethos of the medical profession.     

Heating of tissues by microwaves: A model analysis

We consider the thermal response times for heating of tissue subject to nonionizing (microwave or infrared) radiation. The analysis is based on a dimensionless form of the bioheat equation. The thermal response is governed by two time constants: one(τ₁) pertains to heat convection by blood flow, and is of the order of 20–30 min for physiologically normal perfusion rates; the second (τ₂) characterizes heat conduction and varies as the square of a distance that characterizes the spatial extent of the heating. Two idealized cases are examined. The first is a tissue block with an insulated surface, subject to irradiation with an exponentially decreasing specific absorption rate, which models a large surface area of tissue exposed to microwaves. The second is a hemispherical region of tissue exposed at a spatially uniform specific absorption rate, which models localized exposure. In both cases, the steady-state temperature increase can be written as the product of the incident power density and an effective time constant τ_eff, which is defined for each geometry as an appropriate function of τ₁ and τ₂. In appropriate limits of the ratio of these time constants, the local temperature rise is dominated by conductive or convective heat transport. Predictions of the block model agree well with recent data for the thresholds for perception of warmth or pain from exposure to microwave energy. Using these concepts, we developed a thermal averaging time that might be used in standards for human exposure to microwave radiation, to limit the temperature rise in tissue from radiation by pulsed sources. We compare the ANSI exposure standards for microwaves and infrared laser radiation with respect to the maximal increase in tissue temperature that would be allowed at the maximal permissible exposures. A historical appendix presents the origin of the 6-min averaging time used in the microwave standard. Bioelectromagnetics 19:420–428, 1998. © 1998 Wiley-Liss, Inc.     

海岛生态物联网建设:概念和模型

海岛是自然资源的重要组成部分,但由于受海洋影响强烈、海岛空间有限而生态脆弱性明显,应加强保护。保护的前提则需要掌握海岛生态本底现状及未来发展、变化趋势等信息,海岛生态物联网监测则能够为实现这一需求提供重要支撑。本文在前人相关研究的基础上,概述了海岛生态物联网的概念,即基于物联网技术对海岛生态系统开展自动、实时、长期监测并获取海岛生物、非生物、生态安全等信息以掌握海岛生态系统在自然和人为活动干扰下的变化规律与机制,评估海岛生态状况以作出相应决策和开展海岛生态学研究的基础网络体系;结合海岛特点构建了海岛生态物联网概念模型,形成了由生态要素监测层、数据采集层、存储层、网络传输层、能源保障层、保密层、应用层等7部分构成的监测体系;海岛生态物联网在前期构建、监测内容、数据管理、建设及维护、数据应用等方面具有区别于其他物联网的特征。以广东典型小海岛——三角岛为例展示了海岛生态物联网概念模型在具体海岛上的构建应用,为下一步开展三角岛生态物联网的实践应用及管理提供基础参考,为海岛生态监测和生态物联网建设提供理论和实践参考,并有助于未来海岛生态物联网建设的研究。     

Question 9: Quantum Self-Assembly and Photoinduced Electron Tunneling in Photosynthetic Systems of Artificial Minimal Living Cells

Natural and artificial living cells and their substructures are self-assembling, due to electron correlation interactions among biological and water molecules, which lead to attractive dispersion forces and hydrogen bonds. Dispersion forces are weak intermolecular forces that arise from the attractive force between quantum multipoles. A hydrogen bond is a special type of quantum attractive interaction that exists between an electronegative atom and a hydrogen atom bonded to another electronegative atom; and this hydrogen atom exist in two quantum states. The best method to simulate these dispersion forces and hydrogen bonds is to perform quantum mechanical non-local density functional potential calculations of artificial minimal living cells consisting of around 1,000 atoms. The cell systems studied are based on peptide nucleic acid and are 3.0–4.2 nm in diameter. The electron tunneling and associated light absorption of the most intense transitions, as calculated by the time dependent density functional theory method, differs from spectroscopic experiments by only 0.2–0.3 nm, which is within the value of experiment errors. This agreement implies that the quantum mechanically self-assembled structures of artificial minimal living cells very closely approximate realistic ones.     

Quality-of-life indicators at different scales: Theoretical background

The article is presenting the general analysis of the systems approach and model approaches for the development of QoL indicators and indices. In our study we propose the method of response function as a method of the construction of purposeful, credible integrated models from data and prior knowledge or information. The method of response function implies credible models in the sense that they are identifiable, and, hopefully, explains system output behaviour satisfactorily.Using response function method for the development of QoL models, we are able to obtain QoL indices as the direct output of the models.     

Autoxidation of naphthohydroquinones: Effects of pH,naphthoquinones and superoxide dismutase

The rates of autoxidation of a number of pure naphthohydroquinones have been determined, and the effects of pH, superoxide dismutase (SOD) and of the parent naphthoquinone on the oxidation rates have been investigated. Most compounds were slowly oxidised in acid solution with the rates increasing with increasing pH, although 2-hydroxy-, 2-hydroxy-3-methyl- and 2-amino-1,4-naphthohydroquinone were rapidly oxidised at pH 5 and the rates of oxidation of these substances were comparatively unresponsive to changes in pH. At pH 7.4, autoxidation rates decreased in the order 2,3-dichloro-1,4-naphthohydroquinone > 5-hydroxy > 2-bromo > 2-hydroxy-3-methyl > 2-amino > 2-hydroxy > 2-methoxy > 2,3-dimethoxy > 2,3-dimethyl > 2-methyl > unsubstituted hydroquinone. The autoxidation rates of the alkyl, alkoxy, hydroxy and amino derivatives were decreased in the presence of SOD, but this enzyme had no effect on the rate of autoxidation of the 2,3-dichloro and 2-bromo derivatives while that of the 5-hydroxy derivative was increased. The rates of autoxidation of all compounds except the halogen derivatives and 5-hydroxy-1,4-naphthohydroquinone were increased by addition of the parent naphthoquinone, and quinone addition partially or completely overcame the inhibitory effect of SOD. There is evidence that the reduction of quinones to hydroquinones in vivo may lead either to detoxification or to activation. This may be due to differences in the rate or mechanism of autoxidation of the hydroquinones that are formed, and the data gained in this study will provide a framework for testing this possibility.     

Denaturation and unfolding of human anaphylatoxin C3a: an unusually low covalent stability of its native disulfide bonds

The complement C3a anaphylatoxin is a major molecular mediator of innate immunity. It is a potent activator of mast cells, basophils and eosinophils and causes smooth muscle contraction. Structurally, C3a is a relatively small protein (77 amino acids) comprising a N-terminal domain connected by 3 native disulfide bonds and a helical C-terminal segment. The structural stability of C3a has been investigated here using three different methods: Disulfide scrambling; Differential CD spectroscopy; and Reductive unfolding. Two uncommon features regarding the stability of C3a and the structure of denatured C3a have been observed in this study. (a) There is an unusual disconnection between the conformational stability of C3a and the covalent stability of its three native disulfide bonds that is not seen with other disulfide proteins. As measured by both methods of disulfide scrambling and differential CD spectroscopy, the native C3a exhibits a global conformational stability that is comparable to numerous proteins with similar size and disulfide content, all with mid-point denaturation of [GdmCl]_1/2 at 3.4-5 M. These proteins include hirudin, tick anticoagulant protein and leech carboxypeptidase inhibitor. However, the native disulfide bonds of C3a is 150-1000 fold less stable than those proteins as evaluated by the method of reductive unfolding. The 3 native disulfide bonds of C3a can be collectively and quantitatively reduced with as low as 1 mM of dithiothreitol within 5 min. The fragility of the native disulfide bonds of C3a has not yet been observed with other native disulfide proteins. (b) Using the method of disulfide scrambling, denatured C3a was shown to consist of diverse isomers adopting varied extent of unfolding. Among them, the most extensively unfolded isomer of denatured C3a is found to assume beads-form disulfide pattern, comprising Cys³⁶-Cys⁴⁹ and two disulfide bonds formed by two pair of consecutive cysteines, Cys²²-Cys²³ and Cys⁵⁶-Cys⁵⁷, a unique disulfide structure of polypeptide that has not been documented previously.