Creative dynamics approach to neural intelligence

The thrust of this paper is to introduce and discuss a substantially new type of dynamical system for modelling biological behavior. The approach was motivated by an attempt to remove one of the most fundamental limitations of artificial neural networks — their rigid behavior compared with even simplest biological systems. This approach exploits a novel paradigm in nonlinear dynamics based upon the concept of terminal attractors and repellers. It was demonstrated that non-Lipschitzian dynamics based upon the failure of Lipschitz condition exhibits a new qualitative effect — a multi-choice response to periodic external excitations. Based upon this property, a substantially new class of dynamical systems — the unpredictable systems — was introduced and analyzed. These systems are represented in the form of coupled activation and learning dynamical equations whose ability to be spontaneously activated is based upon two pathological characteristics. Firstly, such systems have zero Jacobian. As a result of that, they have an infinite number of equilibrium points which occupy curves, surfaces or hypersurfaces. Secondly, at all these equilibrium points, the Lipschitz conditions fails, so the equilibrium points become terminal attractors or repellers depending upon the sign of the periodic excitation. Both of these pathological characteristics result in multi-choice response of unpredictable dynamical systems. It has been shown that the unpredictable systems can be controlled by sign strings which uniquely define the system behaviors by specifying the direction of the motions in the critical points. By changing the combinations of signs in the code strings the system can reproduce any prescribed behavior to a prescribed accuracy. That is why the unpredictable systems driven by sign strings are extremely flexible and are highly adaptable to environmental changes. It was also shown that such systems can serve as a powerful tool for temporal pattern memories and complex pattern recognition. It has been demonstrated that new architecture of neural networks based upon non-Lipschitzian dynamics can be utilized for modelling more complex patterns of behavior which can be associated with phenomenological models of creativity and neural intelligence.     

Impact of phosphorus availability on modelling phytoplankton dynamics

Regulation of phosphorus loading is considered to be the primary method of eutrophication control for many lake systems. It is therefore necessary to have accurate estimates of the forms and bioavailability of all phosphorus sources in order to develop the most cost effective load control measures. Research at Clarkson University, aimed at improving the accuracy of estimates of the form and reactivity of phosphorus loadings to Lake Erie, has revealed a significant difference between the algal-availability of allochthonous and autochthonous particulate phosphorus. This paper presents the results of modifying an existing multi-nutrient phytoplankton model by separating allochthonous phosphorus into three forms: soluble reactive phosphorus (SRP) — immediately available for algal uptake; external ultimately-available phosphorus—not immediately available but converted to an available form at a specific rate; an external refractory phosphorus (ERP)—not available while in the water column. Comparisons between the original and modified models showed that the modified phosphorus dynamics proved to be a viable alternative to the concept of invoking an unexplained soluble phosphorus water column loss term, employed in the original model. The work also demonstrates that the distinction is significant for lakes receiving a significant portion of their external phosphorus load in a particulate (not immediately available) form and having a morphometry and hydrology such that this particulate phosphorus remains in the water column for longer than about two weeks.     

Localization of mitochondrial DNA base excision repair to an inner membrane-associated particulate fraction

Mitochondrial DNA (mtDNA) contains high levels of oxidative damage relative to nuclear DNA. A full, functional DNA base excision repair (BER) pathway is present in mitochondria, to repair oxidative DNA lesions. However, little is known about the organization of this pathway within mitochondria. Here, we provide evidence that the mitochondrial BER proteins are not freely soluble, but strongly associated with an inner membrane-containing particulate fraction. Uracil DNA glycosylase, oxoguanine DNA glycosylase and DNA polymerase γ activities all co-sedimented with this particulate fraction and were not dissociated from it by detergent (0.1% or 1.0% NP40) treatment. The particulate associations of these activities were not due to their binding mtDNA, which is itself associated with the inner membrane, as they also localized to the particulate fraction of mitochondria from 143B (TK⁻) ρ⁰ cells, which lack mtDNA. However, all of the BER activities were at least partially solubilized from the particulate fraction by treatment with 150–300 mM NaCl, suggesting that electrostatic interactions are involved in the association. The biological implications of the apparent immobilization of BER proteins are discussed.     

Hume and the argument for biological design

There seems to be a widespread conviction — evidenced, for example, in the work of Mackie, Dawkins and Sober — that it is Darwinian rather than Humean considerations which deal the fatal logical blow to arguments for intelligent design. I argue that this conviction cannot be well-founded. If there are current logically decisive objections to design arguments, they must be Humean — for Darwinian considerations count not at all against design arguments based upon apparent cosmological fine-tuning. I argue, further, that there are good Humean reasons for atheists and agnostics to resist the suggestion that apparent design — apparent biological design and/or apparent cosmological fine-tuning — establishes (or even strongly supports) the hypothesis of intelligent design.     

Disease in marine aquaculture

It has become almost a truism that success in intensive production of animals must be based in part on development of methods for disease diagnosis and control. Excellent progress has been made in methods of diagnosis for major pathogens of cultivated fish, crustacean and molluscan species. In many instances these have proved to be facultative pathogens, able to exert severe effects in populations of animals under other stresses (marginal physical or chemical conditions; overcrowding). The concept of stress management as a critical prophylactic measure is not new, but its significance is being demonstrated repeatedly. The particular relationship of water quality and facultative pathogens such asVibrio, Pseudomonas andAeromonas species has been especially apparent. Virus diseases of marine vertebrates and invertebrates — little known two decades ago — are now recognized to be of significance to aquaculture. Virus infections of oysters, clams, shrimps and crabs have been described, and mortalities have been attributed to them. Several virus diseases of fish have also been recognized as potential or actual problems in culture. In some instances, the pathogens seem to be latent in natural populations, and may be provoked into patency by stresses of artificial environments. One of the most promising approaches to disease prophylaxis is through immunization. Fish respond well to various vaccination procedures, and new non-stressing methods have been developed. Vibriosis — probably the most severe disease of ocean-reared salmon — has been controlled to a great extent through use of a polyvalent bacterin, which can be modified as new pathogenic strains are isolated. Prophylactic immunization for other bacterial diseases of cultivated fish has been attempted, especially in Japan, with some success. There is also some evidence that the larger crustaceans may be immunologically responsive, and that at least short-term protection may be afforded to cultured populations. Some progress has been made in marine disease control through chemical treatment in intensive culture systems, principally through application and modification of methods developed for freshwater aquaculture. Major constraints to use of chemicals are restrictions due to public health concerns about food contamination, and the negative effects of some chemicals on biological filters and on algal food production. There is a continuing need, however, for development of specific treatments for acute disease episodes — such as the nitrofurans, developed in Japan, which are effective for some bacterial diseases. The history of aquaculture — freshwater as well as marine — has been characterized by transfers and introductions of species to waters beyond their present ranges. The process continues, and carries with it the possibility of transfers of pathogens to native species and to the recipient culture environments. International groups are attempting to define codes of practice to govern such mass movements, but examples of introductions of real or potential pathogens already exist. The most recent and the most dramatic is the world wide transfer of a virus pathogen of penaeid shrimps. Earlier examples include the introduction of a protozoan pathogen of salmonids to the western hemisphere, and the introduction of a parasitic copepod from the Far East to the west coast of North America and to France. The conclusion is inevitable — diseases are substantial deterrents to aquaculture production. Diagnostic and control procedures are and will be important components of emerging aquaculture technology.     

Particulate and dissolved phosphorus forms in freshwater: composition and analysis

In recent research, particulate and dissolved phosphorus components have been separated and characterized on the basis of their physical and chemical properties and partly by their origins.Classical operationally defined monitoring variables (dissolved reactive phosphorus, dissolved unreactive phosphorus and particulate phosphorus) are not congruent with known specific physical or chemical components of phosphorus in natural waters or with their bioavailability.Physical isolation of true particles, colloids and molecules of various sizes is possible at present although it is not recommended for routine use.Chemical characterization of particulate phosphorus is performed mainly by sediment extraction procedures (specialized for inorganic species) and — to a lesser degree — by cell extraction procedures (specialized for organic compounds). The extraction procedures are similar and physical preseparation or alternative procedures (e.g. enzymatic assays) are essential.Smaller colloids and dissolved compounds are physically separated by column chromatography and are often chemically characterized by degradation on the addition of specific enzymes.     

Mechanism, origin, and evolution of anoxia tolerance in animals

Organisms vary widely in their tolerance to conditions of limiting oxygen supply to their cells and tissues. A unifying framework of hypoxia tolerance is now available that is based on information from cell-level models from highly anoxia-tolerant species, such as the aquatic turtle, and from other more hypoxia-sensitive systems. The response of hypoxia-tolerant systems to oxygen lack occurs in two (defense and rescue) phases. The first lines of defense against hypoxia include a drastic, if balanced, suppression of ATP demand and supply pathways; this regulation allows ATP levels to remain constant, even while ATP turnover rates greatly decline. The ATP requirements of ion pumping are down-regulated by generalized ‘channel’ arrest in hepatocytes and by the arrest of specific ion channels in neurons. In hepatocytes, the ATP demands of protein synthesis are down-regulated on exposure to hypoxia by an immediate global blockade of the process (probably through translational arrest caused by complexing between polysomes and elongation factors). In hypoxia-sensitive cells, this translational arrest seems irreversible, but hypoxia-tolerant systems activate ‘rescue’ mechanisms if the period of oxygen lack is extended by preferentially regulating the expression of several proteins. In these cells, a cascade of processes underpinning hypoxia rescue and defense begins with an oxygen sensor (a heme protein) and a signal transduction pathway that leads to the specific activation of some genes (increased expression of several proteins) and to specific down-regulation of other genes (decreased expression of several other proteins). The functional roles of the oxygen-sensing and signal-transduction system include significant gene-based metabolic reprogramming — the rescue process — with maintained down-regulation of energy demand and supply pathways in metabolism throughout the hypoxic period. We consider that, through this recent work, it is becoming evident how normoxic-maintenance ATP turnover rates can be down-regulated by an order of magnitude or more — to a new hypometabolic steady state, which is prerequisite for surviving prolonged hypoxia or anoxia. Because the phylogenies of the turtles and of fishes are well known, we are now in an excellent position to assess conservative vs. adaptable features in the evolution of the above hypoxia-response physiology in these two specific animal lineages.     

Membranes of animal cells. II. The metabolism and turnover of the surface membrane

Turnover studies of the surface membrane and of cell particulate matter of L cells in tissue culture in logarithmic and plateau phase of growth have been made. The rate of incorporation of isotope into these fractions and the rate of fall of specific activities of labeled L-cell fractions have been observed. The following interpretation of the data appears most likely although other interpretations are possible. Growing and nongrowing cells synthesize approximately similar amounts of surface membrane and particulate material. In the growing cell the material is incorporated with net increases in substance. There is relatively little turnover. In the nongrowing cell newly synthesized material is incorporated, but a corresponding amount of material is eliminated so that there is turnover without net increase of substance. Our results suggest that there is no gross differential turnover between the protein, lipid, and carbohydrate of the surface membrane under the conditions of our experiments. Metabolic inhibitors or omission of amino acids in the culture medium lead to a decrease in synthesis of surface membrane and cell particulates and cause an equivalent decrease in the rate of degradation of surface membrane and of particulates; therefore the synthetic and degradative aspects of turnover appear to be coupled. As cultures of nongrowing cells in suspension or on a glass surface age, their synthetic and turnover capacities diminish. Our results suggest that the cell may exist in a nongrowing state with a level of synthesis similar to that of a growing cell. It can exist in this state with a high level of turnover.     

The Enantiomer of Cholesterol

Cholesterol plays a variety of significant roles in biological systems. However, the mechanisms by which cholesterol functions remain largely unclear. The enantiomer of cholesterol (ent-cholesterol)—which has identical physical properties, but opposite three-dimensional configuration compared to cholesterol—is a unique tool that can be used to better understand the mechanisms of cholesterol function. We review the literature pertaining to ent-cholesterol, focusing in particular on its use in biological studies.     

Particulate inputs to Dublin Bay and to the South Lagoon,Bull Island

There are substantial riverine and sewage particulate inputs into Dublin Bay. The main river, the R. Liffey, accounts for almost 85% of the riverine input, which amounts to 37.1 t d^–1 of SPM. The sewage input, which is discharged into the estuary, is slightly less at 35.3 t d^–1. The combined inputs deliver 17.4 t d^–1, 2.9 t d^–1and 1.2 t d^–1of particulate C, N and P, respectively, to the Bay as a whole. Although the particulate N load accounts for just 20% of the total N input, the retention of particulates within the system, and the subsequent remobilisation of N from the sediments is heavily implicated in the macroalgal blooms. A particulate mass balance of SPM, and of C, N and P for the South Lagoon showed no consistent pattern of import/export except that the fluxes of the individual elements reflected SPM load and varied with quantity rather than quality. The molar C:N ratio was around 6:1 although on occasion values approaching 3:1 were obtained, indicating very high quality and potentially labile SPM. The controlling factors in the budget appeared to be the water velocities and to a lesser extent, the SPM load, which surprisingly was no greater on a spring tide than on a neap. In this shallow, and primarily intertidal, system, wind- or wave-driven resuspension may exert more influence than predictable factors such as tidal range.     

Characterization and Deposition of Respirable Large- and Small-Particle Bioaerosols

The deposition patterns of large-particle microbiological aerosols within the respiratory tract are not well characterized. A novel system (the flow-focusing aerosol generator [FFAG]) which enables the generation of large (>10-μm) aerosol particles containing microorganisms under laboratory conditions was characterized to permit determination of deposition profiles within the murine respiratory tract. Unlike other systems for generating large aerosol particles, the FFAG is compatible with microbiological containment and the inhalational challenge of animals. By use of entrapped Escherichia coli cells, Bacillus atrophaeus spores, or FluoSphere beads, the properties of aerosols generated by the FFAG were compared with the properties of aerosols generated using the commonly available Collison nebulizer, which preferentially generates small (1- to 3-μm) aerosol particles. More entrapped particulates (15.9- to 19.2-fold) were incorporated into 9- to 17-μm particles generated by the FFAG than by the Collison nebulizer. The 1- to 3-μm particles generated by the Collison nebulizer were more likely to contain a particulate than those generated by the FFAG. E. coli cells aerosolized using the FFAG survived better than those aerosolized using the Collison nebulizer. Aerosols generated by the Collison nebulizer and the FFAG preferentially deposited in the lungs and nasal passages of the murine respiratory tract, respectively. However, significant deposition of material also occurred in the gastrointestinal tract after inhalation of both the small (89.7%)- and large (61.5%)-particle aerosols. The aerosols generated by the Collison nebulizer and the FFAG differ with respect to mass distribution, distribution of the entrapped particulates, bacterial survival, and deposition within the murine respiratory tract.     

The physical chemistry of hemes and hemopeptides III. Synthesis and physicochemical properties of cytochrome c-related heme-pentapeptide soluble in organic solvents

Synthesis is described of a N_α- and C-protected pentapeptide (Cys—Gly—Gly—Cys—His) which corresponds to the segment 14–18 in the primary structure of cytochrome c. The preparation of hemipentapeptide which contains peptide covalently linked to 2.4 side chains of the tetrapyrrolic ring is described.The hemipentapeptide is soluble in organic solvents and can be reduced in heterogeneous solvent mixture. In benzene its absorption and EPR spectra show that the iron ion is a high spin state. The titration of model compound in the oxidized and reduced forms was followed by optical absorption and it indicates a one-base fixation to form hexacoordinated complexes showing the presence of histidine residue liganded to the iron ion in the hemichrome and hemochrome obtained. The stability constants are 1.3 · 10³ and 1.7 · 10³ l/mole, respectively.From these results and by analogy with the absorption spectra of biological systems or others models, the presence of histidine residue on iron ion in the model compound is discussed.     

Coliphages and enteric viruses in the particulate phase of river water

The present study was undertaken to determine if indigenous enteric viruses and coliphages are free or associated with suspended particulate matter in natural waters. River water was filtered on filters of decreasing porosities (100-0.25 micron) that were pretreated with detergent to eliminate viral adsorption while retaining particulates. This filtered water was refiltered in virus-adsorbing conditions to retain free viruses. The virus-adsorbing filter retained most of the enteric viruses (77.4%) and coliphages (65.8%), which indicated that these viruses were probably free or associated with particles with a diameter of less than 0.25 micron. These observations are important because in water treatment plants small particulates are often the most difficult to eliminate.     

Xanthan production byXanthomonas campestris in continuous fermentation

Summary Xanthan production by a strain ofX. campestris was maintained longer under glucose—limited than nitrogen—limited conditions in continuous culture. The turnover Q was 12 at lower pH(5.0–6.0) and 6.5 at neutral pH; xanthan productivity was comparable at both pH in nitrogen—limited continuous cultures. In the Fe—rich continuous fermentation cell degeneration did not occur for 65 turnovers whereas in the Fe—deficient fermentation it occurred in 12 turnovers. The culture stability for xanthan formation is higher under conditions which are favorable for cell growth with limited xanthan production.     

Microbial methanol uptake in northeast Atlantic waters

Methanol is the predominant oxygenated volatile organic compound in the troposphere, where it can significantly influence the oxidising capacity of the atmosphere. However, we do not understand which processes control oceanic concentrations, and hence, whether the oceans are a source or a sink to the atmosphere. We report the first methanol loss rates in seawater by demonstrating that ¹⁴C-labelled methanol can be used to determine microbial uptake into particulate biomass, and oxidation to ¹⁴CO₂. We have found that methanol is used predominantly as a microbial energy source, but also demonstrated its use as a carbon source. We report biological methanol oxidation rates between 2.1 and 8.4 nmol l⁻¹ day⁻¹ in surface seawater of the northeast Atlantic. Kinetic experiments predict a V_max of up to 29 nmol l⁻¹ day⁻¹, with a high affinity K_m constant of 9.3 n in more productive coastal waters. We report surface concentrations of methanol in the western English channel of 97±8 n (n=4) between May and June 2010, and for the wider temperate North Atlantic waters of 70±13 n (n=6). The biological turnover time of methanol has been estimated between 7 and 33 days, although kinetic experiments suggest a 7-day turnover in more productive shelf waters. Methanol uptake rates into microbial particles significantly correlated with bacterial and phytoplankton parameters, suggesting that it could be used as a carbon source by some bacteria and possibly some mixotrophic eukaryotes. Our results provide the first methanol loss rates from seawater, which will improve the understanding of the global methanol budget.     

Spherules in the serology of Coccidioides immitis. II. Complement fixation tests with human sera

Soluble and particulate spherule antigens fixed complement in tests with anti—C. immitis sera. However, the soluble antigen proved more active than the particulate one. Cross reactions were noted between the spherule antigens and anti—H. capsulatum and anti—B. dermatitidis sera. Following enzymatic treatment of the particulate preparation a soluble antigen was obtained which formed two bands with anti—C. immitis serum and one band with anti-H. capsulatum serum in an agar gel double diffusion test.     

Chiral escape of bark beetles from predators responding to a bark beetle pheromone

Summary Two species of predatory beetles that locate their prey, Ips pini, by responding to its aggregation pheromone have different chiral preferences to ispdienol than does the herbivore. This suggests that chiral disparity may provide some escape for bark beetles from predation, and that geographic variation in herbivore communication systems may be partially due to predator — imposed selection pressures. These results also suggest ways in which the semiochemical and biological control of North America's most damaging group of forest insects can be improved.     

A new interpretation of plasmodesmatal ultrastructure

Summary It is shown that simple, unbranched, plasmodesmata between young xylem ray cells of willow have no direct intercellular continuity apart from the plasmalemma which limits the cytoplasm and lines the plasmodesmatal canal. Each plasmodesma is traversed by a 200 Å diameter tubule (the desmotubule) which has a wall with probably 11 subunits arranged around a central cavity through which runs a 40 Å diameter rod. This rod is connected to the inside of the tubule wall, by fine filaments. At the ends of each plasmodesma the plasmalemma and cell wall are closely appressed to the tubule, thus precluding direct continuity between the cytoplasm of adjacent cells. Through the central part of the plasmodesmata the tubule is separated from the plasmalemma by a 90–100 Å wide gap. Cytoplasmic microtubules in the same tissue have a diameter of approximately 250 Å and a wall probably composed of 13 subunits: both desmotubules and cytoplasmic microtubules therefore have a centre-to-centre subunit spacing of about 47 Å. It is suggested that the desmotubules are not microtubules but may be nuclear spindle fibres which become trapped in the wall during cell plate formation. The endoplasmic reticulum, while closely approaching the plasmodesmata, is not continuous across them. It is thought most unlikely that the endoplasmic reticulum traverses plasmodesmata, as the dimensions of the central tubule — found here as well as by other workers — are smaller than those which would be expected to allow a stable molecular configuration in a unit membrane. The plasmalemma, where it lines the plasmodesmatal canal, appears to have particulate subunits in the outer opaque layers and the presence of these subunits may be attributable to the need for stability in membranes arranged about so small a radius.     

Comparative morphology of acrogenous branch systems and phylogenetic considerations. II. Angiosperms

A concept for a primitive angiospermous branch system is given in order to have a starting point for the derivation of the diverse and highly differentiated branch systems observed in contemporary angiosperms. Hitherto Troll's (1964, 1969) comparative study of the synflorescences in this plant group — developed out predominantly on herbaceous plants — was the most comprehensive and sophisticated treatment dealing with branch systems. Unfortunately, the work on tropical tree architecture by Hallé et al. (1978) has no reference to the classical studies of Troll and his pupils. Thus Müller-Doblies and Weberling (1984) emphasized the high degree of terminological incompatibility between the two works. Angiosperms are seen as a monophyletic plant division. Consequently, the branch system of the first primitive angiosperms must be the starting point in the evolution of the abundant diversity of branch systems and growth forms of modern angiosperms. If it is accepted that primitive angiospermous shoots were terminated by a large flower, one may assume, that the reproductive end of the shoot was enriched by paracladia early in evolution, thereby developing a terminal inflorescence instead of a single flower. Thus the primitive shoot unit was divided into a basal vegetative region — the trophotagma, branching retardively — and the reproductive terminal region, the anthotagma, branching simultaneously. It is demonstrated through a selection of different examples, that the construction of such a system possesses the options for several modifications, enabling the evolution of the abundant diversity of branch systems which characterizes contemporary angiosperms.