A knowledge-based evolution strategy for the multi-objective minimum spanning tree problem

A fast Knowledge-based Evolution Strategy, KES, for the multi-objective minimum spanning tree, is presented. The proposed algorithm is validated, for the bi-objective case, with an exhaustive search for small problems (4-10 nodes), and compared with a deterministic algorithm, EPDA and NSGA-II for larger problems (up to 100 nodes) using benchmark hard instances. Experimental results show that KES finds the true Pareto fronts for small instances of the problem and calculates good approximation Pareto sets for larger instances tested. It is shown that the fronts calculated by YES are superior to NSGA-II fronts and almost as good as those established by EPDA. KES is designed to be scalable to multi-objective problems and fast due to its small complexity.

Perspex machine VII: The universal perspex machine

The perspex machine arose from the unification of projective geometry with the Turing machine. It uses a total arithmetic, called transreal arithmetic, that contains real arithmetic and allows division by zero. Transreal arithmetic is redefined here. The new arithmetic has both a positive and a negative infinity which lie at the extremes of the number line, and a number nullity that lies off the number line. We prove that nullity, 0/0, is a number. Hence a number may have one of four signs: negative, zero, positive, or nullity. It is, therefore, impossible to encode the sign of a number in one bit, as floating-, point arithmetic attempts to do, resulting in the difficulty of having both positive and negative zeros and NaNs. Transrational arithmetic is consistent with Cantor arithmetic. In an extension to real arithmetic, the product of zero, an infinity, or nullity with its reciprocal is nullity, not unity. This avoids the usual contradictions that follow from allowing division by zero. Transreal arithmetic has a fixed algebraic structure and does not admit options as IEEE, floating-point arithmetic does. Most significantly, nullity has a simple semantics that is related to zero. Zero means "no value" and nullity means "no information." We argue that nullity is as useful to a manufactured computer as zero is to a human computer. The perspex machine is intended to offer one solution to the mind-body problem by showing how the computable aspects of mind and. perhaps, the whole of mind relates to the geometrical aspects of body and, perhaps, the whole of body. We review some of Turing's writings and show that he held the view that his machine has spatial properties. In particular, that it has the property of being a 7D lattice of compact spaces. Thus, we read Turing as believing that his machine relates computation to geometrical bodies. We simplify the perspex machine by substituting an augmented Euclidean geometry for projective geometry. This leads to a general-linear perspex-machine which is very much easier to pro-ram than the original perspex-machine. We then show how to map the whole of perspex space into a unit cube. This allows us to construct a fractal of perspex machines with the cardinality of a real-numbered line or space. This fractal is the universal perspex machine. It can solve, in unit time, the halting problem for itself and for all perspex machines instantiated in real-numbered space, including all Turing machines. We cite an experiment that has been proposed to test the physical reality of the perspex machine's model of time, but we make no claim that the physical universe works this way or that it has the cardinality of the perspex machine. We leave it that the perspex machine provides an upper bound on the computational properties of physical things, including manufactured computers and biological organisms, that have a cardinality no greater than the real-number line.

A hybridised evolutionary algorithm for multi-criterion minimum spanning tree problems

A hybridised and Knowledge-based Evolutionary Algorithm (KEA) is applied to the multi-criterion minimum spanning tree problems. Hybridisation is used across its three phases. In the first phase a deterministic single objective optimization algorithm finds the extreme points of the Pareto front. In the second phase a K-best approach finds the first neighbours of the extreme points, which serve as an elitist parent population to an evolutionary algorithm in the third phase. A knowledge-based mutation operator is applied in each generation to reproduce individuals that are at least as good as the unique parent. The advantages of KEA over previous algorithms include its speed (making it applicable to large real-world problems), its scalability to more than two criteria, and its ability to find both the supported and unsupported optimal solutions.

Global climate change and tree nutrition: effects of elevated CO2 and temperature

Although tree nutrition has not been the primary focus of large climate change experiments on trees, we are beginning to understand its links to elevated atmospheric CO2 and temperature changes. This review focuses on the major nutrients, namely N and P, and deals with the effects of climate change on the processes that alter their cycling and availability. Current knowledge regarding biotic and abiotic agents of weathering, mobilization and immobilization of these elements will be discussed. To date, controlled environment studies have identified possible effects of climate change on tree nutrition. Only some of these findings, however, were verified in ecosystem scale experiments. Moreover, to be able to predict future effects of climate change on tree nutrition at this scale, we need to progress from studying effects of single factors to analysing interactions between factors such as elevated CO2, temperature or water availability.

Recent patterns of change in vegetation structure and tree composition of British broadleaved woodland: evidence from large-scale surveys

Evidence is presented of widespread changes in structure and species composition between the 1980s and 2003–2004 from surveys of 249 British broadleaved woodlands. Structural components examined include canopy cover, vertical vegetation profiles, field-layer cover and deadwood abundance. Woods were located in 13 geographical localities and the patterns of change were examined for each locality as well as across all woods. Changes were not uniform throughout the localities; overall, there were significant decreases in canopy cover and increases in sub-canopy (2–10 m) cover. Changes in 0.5–2 m vegetation cover showed strong geographic patterns, increasing in western localities, but declining or showing no change in eastern localities. There were significant increases in canopy ash Fraxinus excelsior and decreases in oak Quercus robur/petraea. Shrub layer ash and honeysuckle Lonicera periclymenum increased while birch Betula spp. hawthorn Crataegus monogyna and hazel Corylus avellana declined. Within the field layer, both bracken Pteridium aquilinum and herbs increased. Overall, deadwood generally increased. Changes were consistent with reductions in active woodland management and changes in grazing and browsing pressure. These findings have important implications for sustainable active management of British broadleaved woodlands to meet silvicultural and biodiversity objectives.

A universal primer for isolation of fragments of a gene encoding phytoene desaturase for use in virus-induced gene silencing (VIGS) studies

We have been using Virus-Induced Gene Silencing (VIGS) to test the function of genes that are candidates for involvement in floral senescence. Although VIGS is a powerful tool for assaying the effects of gene silencing in plants, relatively few taxa have been studied using this approach, and most that have are in the Solanaceae. We typically use silencing of phytoene desaturase (PDS) in preliminary tests of the feasibility of using VIGS. Silencing this gene, whose product is involved in carotene biosynthesis, results in a characteristic photobleaching phenotype in the leaves. We have found that efficient silencing requires the use of fragments that are more than 90% homologous to the target gene. To simplify testing the effectiveness of VIGS in a range of species, we designed a set of universal primers to a region of the PDS gene that is highly conserved among species, and that therefore allows an investigator to isolate a fragment of the homologous PDS gene from the species of interest. We report the sequences of these primers and the results of VIGS experiments in horticultural species from the Asteraceae, Leguminosae, Balsaminaceae and Solanaceae.

Biomass partitioning and growth efficiency in four naturally regenerated forest tree species

Current forest growth models and yield tables are almost exclusively based on data from mature trees, reducing their applicability to young and developing stands. To address this gap, young European beech, sessile oak, Scots pine and Norway spruce trees approximately 0 to 10 years old were destructively sampled in a range of naturally regenerated forest stands in Central Europe. Diameter at base and height were first measured in situ for up to 175 individuals per species. Subsequently, the trees were excavated and dry biomass of foliage, branches, stems and roots was measured. Allometric relations were then used to calculate biomass allocation coefficients (BAC) and growth efficiency (GE) patterns in young trees. We found large differences in BAC and GE between broadleaves and conifers, but also between species within these categories. Both BAC and GE are strongly age-specific in young trees, their rapidly changing values reflecting different growth strategies in the earliest stages of growth. We show that linear relationships describing biomass allocation in older trees are not applicable in young trees. To accurately predict forest biomass and carbon stocks, forest growth models need to include species and age specific parameters of biomass allocation patterns.

Tree species’ tolerance to water stress, salinity and fire

According to climate change predictions, water availability might change dramatically in Europe and adjacent regions. This change will undoubtedly have an adverse effect on existing tree species and affect their ability to cope with a lack or an excess of water, changes in annual precipitation patterns, soil salinity and fire disturbance. The following chapter will describe tree species and proven-ances used in European forestry practice which are the most suitable to deal with water stress, salinity and fire. Each subchapter starts with a brief description of each of the stress factors and discusses the predictions of the likelihood of their occurrence in the near future according to the climate change scenarios. Tree spe-cies and their genotypes able to cope with particular stress factor, together with indication of their use by forest managers are then introduced in greater detail.

Adaptation of tree growth to elevated CO2: quantitative trait loci for biomass in Populus

Information on the genetic variation of plant response to elevated CO2 (e[CO2]) is needed to understand plant adaptation and to pinpoint likely evolutionary response to future high atmospheric CO2 concentrations.• Here, quantitative trait loci (QTL) for above- and below-ground tree growth were determined in a pedigree – an F2 hybrid of poplar (Populus trichocarpa and Populus deltoides), following season-long exposure to either current day ambient CO2 (a[CO2]) or e[CO2] at 600 µl l−1, and genotype by environment interactions investigated.• In the F2 generation, both above- and below-ground growth showed a significant increase in e[CO2]. Three areas of the genome on linkage groups I, IX and XII were identified as important in determining above-ground growth response to e[CO2], while an additional three areas of the genome on linkage groups IV, XVI and XIX appeared important in determining root growth response to e[CO2].• These results quantify and identify genetic variation in response to e[CO2] and provide an insight into genomic response to the changing environment

In vitro gas production and nitrogen degradability of tannin-containing tree fruits in response to incremental levels of polyethylene glycol

This study was designed to determine the response of in vitro fermentation parameters to incremental levels of polyethylene glycol (PEG) when tanniniferous tree fruits (Dichrostachys cinerea, Acacia erioloba, A. erubiscens, A. nilotica and Piliostigma thonningii) were fermented using the Reading Pressure Technique. The trivalent ytterbium precipitable phenolics content of fruit substrates ranged from 175 g/kg DM in A. erubiscens to 607 g/kg DM in A. nilotica, while the soluble condensed tannin content ranged from 0.09 AU550nm/40mg in A. erioloba to 0.52 AU550nm/40 mg in D. cinerea. The ADF was highest in P. thonningii fruits (402 g/kg DM) and lowest in A. nilotica fruits (165 g/kg DM). Increasing the level of PEG caused an exponential rise to a maximum (asymptotic) for cumulative gas production, rate of gas production and nitrogen degradability in all substrates except P. thonningii fruits. Dry matter degradability for fruits containing higher levels of soluble condensed tannins (D. cinerea and P. thonningii), showed little response to incremental levels of PEG after incubation for 24 h. The minimum levels of PEG required to maximize in vitro fermentation of tree fruits was found to be 200 mg PEG/g DM of sample for all tree species except A. erubiscens fruits, which required 100 mg PEG/g DM sample. The study provides evidence that PEG levels lower than 1 g/g DM sample can be used for in vitro tannin bioassays to reduce the cost of evaluating non-conventional tanniniferous feedstuffs used in developing countries in the tropics and subtopics. The use of in vitro nitrogen degradability in place of the favoured dry matter degradability improved the accuracy of PEG as a diagnostic tool for tannins in in vitro fermentation systems.