How to study consciousness scientifically.

The neurosciences have advanced to the point that we can now treat consciousness as a scientific problem like any other. The problem is to explain how brain processes cause consciousness and how consciousness is realized in the brain. Progress is impeded by a number of philosophical mistakes, and the aim of this paper is to remove nine of those mistakes: (i) consciousness cannot be defined; (ii) consciousness is subjective but science is objective; (iii) brain processes cannot explain consciousness; (iv) the problem of ''qualia'' should be set aside; (v) consciousness is epiphenomenal; (vi) consciousness has no evolutionary function; (vii) a causal account of consciousness is necessarily dualistic; (viii) science is reductionistic, so a scientific account of consciousness would show it reducible to something else; and (ix) an account of consciousness must be an information processing account.     

Applying population-genetic models in theoretical evolutionary epidemiology

Much of the existing theory for the evolutionary biology of infectious diseases uses an invasion analysis approach. In this Ideas and Perspectives article, we suggest that techniques from theoretical population genetics can also be profitably used to study the evolutionary epidemiology of infectious diseases. We highlight four ways in which population-genetic models provide benefits beyond those provided by most invasion analyses: (i) they can make predictions about the rate of pathogen evolution; (ii) they explicitly draw out the mechanistic way in which the epidemiological dynamics feed into evolutionary change, and thereby provide new insights into pathogen evolution; (iii) they can make predictions about the evolutionary consequences of non-equilibrium epidemiological dynamics; (iv) they can readily incorporate the effects of multiple host dynamics, and thereby account for phenomena such as immunological history and/or host co-evolution.     

Do hormonal control systems produce evolutionary inertia?

Hormonal control systems are complex in design and well integrated. Concern has been raised that these systems might act as evolutionary constraints when animals are subject to anthropogenic environmental change. Three systems are examined in vertebrates, especially birds, that are important for assessing this possibility: (i) the hypothalamic-pituitary-gonadal (HPG) axis, (ii) the activational effects of sex steroids on mating effort behaviour, and (iii) sexual differentiation. Consideration of how these systems actually work that takes adequate account of the brain's role and mechanisms suggests that the first two are unlikely to be impediments to evolution. The neural and molecular networks that regulate the HPG provide both phenotypic and evolutionary flexibility, and rapid evolutionary responses to selection have been documented in several species. The neuroendocrine and molecular cascades for behaviour provide many avenues for evolutionary change without requiring a change in peripheral hormone levels. Sexual differentiation has some potential to be a source of evolutionary inertia in birds and could contribute to the lack of diversity in certain reproductive (including life history) traits. It is unclear, however, whether that lack of diversity would impede adaptation to rapid environmental change given the role of behavioural flexibility in avian reproduction.     

Natural hybridization and the evolution of domesticated, pest and disease organisms

The role of natural hybridization in the evolutionary history of numerous species is well recognized. The impact of introgressive hybridization and hybrid speciation has been documented especially in plant and animal assemblages. However, there remain certain areas of investigation for which natural hybridization and its consequences remain under-studied and under-appreciated. One such area involves the evolution of organisms that positively or negatively affect human populations. In this review, I highlight exemplars of how natural hybridization has contributed to the evolution of (i) domesticated plants and animals; (ii) pests; (iii) human disease vectors; and (iv) human pathogens. I focus on the effects from genetic exchange that may lead to the acquisition of novel phenotypes and thus increase the beneficial or detrimental (to human populations) aspects of the various taxa.     

Influence of gender and estrous cycle on plasma and renal catecholamine levels in rats

Several studies have demonstrated that gonadal hormones show significant effects on the brain and signaling pathways of effector organs/cells that respond to neurotransmitters. Since little information is available concerning the impact of male and female gonadal hormones on the renal and peripheral sympathetic system, the objective of this study was to further assess whether and how the renal content and plasma concentration of catecholamines are influenced by gender and the estrous cycle in rats. To achieve this, males Wistar rats were divided into 4 groups: (i) sham (i.e., control), (ii) gonadectomized, (iii) gonadectomized and nandrolone decanoate replacement at physiological levels or (iv) gonadectomized and nandrolone decanoate replacement at high levels. Female Wistar rats were divided into 6 groups: (i) ovariectomized (OVX), (ii) estrogen replacement at physiological levels and (iii) estrogen replacement at at high levels, (iv) progesterone replacement at physiological levels and (v) progesterone replacement at at high levels, and (vi) sham. The sham group was subdivided into four subgroups: (i) proestrus, (ii) estrus, (iii) metaestrus, and (iv) diestrus. Ten days after surgery, the animals were sacrificed and their plasma and renal catecholamine levels measured for intergroup comparisons. Gonadectomy led to an increase in the plasma catecholamine concentration in females, as well as in the renal catecholamine content of both male and female rats. Gonadectomized males also showed a lower level of plasma catecholamine than the controls. The urinary flow, and the fractional excretion of sodium and chloride were significantly increased in gonadectomized males and in the OVX group when compared with their respective sham groups.     

Endocrine disruptors: present issues, future directions

A variety of natural products and synthetic chemicals, known collectively as endocrine-disrupting compounds (EDCs), mimic or interfere with the mechanisms that govern vertebrate reproductive development and function. At present, research has focused on (i) the morphological and functional consequences of EDCs; (ii) identifying and determining the relative potencies of synthetic and steroidal compounds that have endocrine-disrupting effects; (iii) the mechanism of action of EDCs at the molecular level; and (iv) the recognition that in "real life," contamination usually reflects mixtures of EDCs. Future research must examine (i) the interactive nature of EDCs, particularly whether the threshold concept as developed in traditional toxicological research applies to these chemicals; (ii) when and how EDCs act at the physiological level, particularly how they may organize the neural substrates of reproductive physiology and behavior; (iii) the various effects these compounds have on different species, individuals, and even tissues; and (iv) how adaptations may evolve in natural populations with continued exposure to EDCs. Several predictions are offered that reflect these new perspectives. Specifically, (i) the threshold assumption will be found not to apply to EDCs because they mimic the actions of endogenous molecules (e.g., estrogen) critical to development; hence, the threshold is automatically exceeded with exposure. (ii) Behavior can compound and magnify the effects of EDCs over successive generations; that is, bioaccumulated EDCs inherited from the mother not only influence the morphological and physiological development of the offspring but also the offsprings' reproductive behavior as adults. This adult behavior, in turn, can have further consequences on the sexual development of their own young. (iii) The sensitivity of a species or an individual to a compound is related to species (individual)-typical concentrations of circulating gonadal steroid hormones. Related to this is the recent finding that alternate forms of the putative receptors are differentially distributed, thereby contributing to the different effects that have been observed. (iv) Except in extraordinary situations, populations often continue to exist in contaminated sites. One possible explanation for this observation that needs to be considered is that animals can rapidly adapt to the nature and level of contamination in their environment. It is unlikely that successive generations coincidentally become insensitive to gonadal steroid hormones fundamentally important as biological regulators of development and reproduction. Rather, adaptive alterations in the genes that encode steroid receptors may occur with chronic exposure to EDCs, allowing the sex hormone receptor to discriminate natural steroids from EDCs.     

Improving assessment and modelling of climate change impacts on global terrestrial biodiversity

Understanding how species and ecosystems respond to climate change has become a major focus of ecology and conservation biology. Modelling approaches provide important tools for making future projections, but current models of the climate-biosphere interface remain overly simplistic, undermining the credibility of projections. We identify five ways in which substantial advances could be made in the next few years: (i) improving the accessibility and efficiency of biodiversity monitoring data, (ii) quantifying the main determinants of the sensitivity of species to climate change, (iii) incorporating community dynamics into projections of biodiversity responses, (iv) accounting for the influence of evolutionary processes on the response of species to climate change, and (v) improving the biophysical rule sets that define functional groupings of species in global models.     

Variation within and among species in gene expression: raw material for evolution

Heritable variation in regulatory or coding regions is the raw material for evolutionary processes. The advent of microarrays has recently promoted examination of the extent of variation in gene expression within and among taxa and examination of the evolutionary processes affecting variation. This review examines these issues. We find: (i) microarray-based measures of gene expression are precise given appropriate experimental design; (ii) there is large inter-individual variation, which is composed of a minor nongenetic component and a large heritable component; (iii) variation among populations and species appears to be affected primarily by neutral drift and stabilizing selection, and to a lesser degree by directional selection; and (iv) neutral evolutionary divergence in gene expression becomes nonlinear with greater divergence times due to functional constraint. Evolutionary analyses of gene expression reviewed here provide unique insights into partitioning of regulatory variation in nature. However, common limitations of these studies include the tendency to assume a linear relationship between expression divergence and species divergence, and failure to test explicit hypotheses that involve the ecological context of evolutionary divergence.     

Characteristics of climate change refugia for Australian biodiversity

Identifying refugia is a critical component of effective conservation of biodiversity under anthropogenic climate change. However, despite a surge in conceptual and practical interest, identifying refugia remains a significant challenge across diverse continental landscapes. We provide an overview of the key properties of refugia that promote species' persistence under climate change, including their capacity to (i) buffer species from climate change; (ii) sustain long‐term population viability and evolutionary processes; (iii) minimize the potential for deleterious species interactions, provided that the refugia are (iv) available and accessible to species under threat. Further, we classify refugia in terms of the environmental and biotic stressors that they provide protection from (i.e. thermal, hydric, cyclonic, pyric and biotic refugia), but ideally refugia should provide protection from a multitude of stressors. Our systematic characterization of refugia facilitates the identification of refugia in the Australian landscape. Challenges remain, however, specifically with respect to how to assess the quality of refugia at the level of individual species and whole species assemblages. It is essential that these challenges are overcome before refugia can live up to their acclaim as useful targets for conservation and management in the context of climate change.     

Elevational diversity patterns as an example for evolutionary and ecological dynamics in ferns and lycophytes

Evolutionary processes such as adaptation, ecological filtering, and niche conservatism involve the interaction of organisms with their environment and are thus commonly studied along environmental gradients. Elevational gradients have become among the most studied environmental gradients to understand large-scale patterns of species richness and composition because they are highly replicated with different combinations of geographical, environmental and historical factors. We here review the literature on using elevational gradients to understand evolutionary processes in ferns. Some phylogenetic studies of individual fern clades have considered elevation in the analysis or interpretation and postulated that fern diversification is linked to the colonization of mountain habitats. Other studies that have linked elevational community composition and hence ecological filtering with phylogenetic community composition and morphological traits, usually only found limited phylogenetic signal. However, these studies are ultimately only correlational, and there are few actual tests of the evolutionary mechanisms leading to these patterns. We identify a number of challenges for improving our understanding of how evolutionary and ecological processes are linked to elevational richness patterns in ferns: i) limited information on traits and their ecological relevance, ii) uncertainties on the dispersal kernels of ferns and hence the delimitation of regional species pools from which local assemblages are recruited, iii) limited genomic data to identify candidate genes under selection and hence actually document adaptation and selection, and iv) conceptual challenges in developing clear and testable hypotheses to how specific evolutionary processes can be linked to patterns in community composition and species richness.     

The Spanish co-operation programme in Equatorial Guinea: a ten-year review of research and nature conservation in Bioko

The Research and Nature Conservation Programme in Equatorial Guinea was launched in 1985, financed by the Spanish Technical Co-operation Agency. The Programme's main objectives were to: (i) increase scientific research; (ii) set up a Museum of Natural History for the country; (iii) update environmental legislation; (iv) create a network of protected natural areas; (v) promote Equatorial Guinea's participation in international forums on the environment; (vi) train local personnel and (vii) implement environmental education programmes. Actions undertaken and results obtained over a ten-year period are reviewed herein. The Programme has been important in raising the level of scientific awareness of the country's resources but more importantly, it has catalysed the inception of the country's existing legal framework for environmental protection (Ley 8/1988). Within this law, regulations with respect to wildlife, protected areas and hunting were promulgated. These include the legal basis to create other reserve areas and non-profit organizations related to wildlife protection. The Programme has been able to employ the law to stop exploitation and road-building along the south of Bioko.     

Current status of antisense DNA methods in behavioral studies

The antisense DNA method has been used successfully to block the expression of specific genes in vivo in neuronal systems. An increasing number of studies in the last few years have shown that antisense DNA administered directly into the brain can modify various kinds of behaviors. These findings strongly suggest that the antisense DNA method can be used as a powerful tool to study causal relationships between molecular processes in the brain and behavior. In this article we review the current status of the antisense method in behavioral studies and discuss its potentials and problems by focusing on the following four aspects; (i) optimal application paradigms of antisense DNA methods in behavioral studies; (ii) efficiencies of different administration methods of antisense DNA used in behavioral studies; (iii) determination of specificity of behavioral effects of antisense DNA; and (iv) discrepancies between antisense DNA effects on behaviors and those on protein levels of the targeted gene.      

A Large-Scale Assessment of Nucleic Acids Binding Site Prediction Programs

Computational prediction of nucleic acid binding sites in proteins are necessary to disentangle functional mechanisms in most biological processes and to explore the binding mechanisms. Several strategies have been proposed, but the state-of-the-art approaches display a great diversity in i) the definition of nucleic acid binding sites; ii) the training and test datasets; iii) the algorithmic methods for the prediction strategies; iv) the performance measures and v) the distribution and availability of the prediction programs. Here we report a large-scale assessment of 19 web servers and 3 stand-alone programs on 41 datasets including more than 5000 proteins derived from 3D structures of protein-nucleic acid complexes. Well-defined binary assessment criteria (specificity, sensitivity, precision, accuracy…) are applied. We found that i) the tools have been greatly improved over the years; ii) some of the approaches suffer from theoretical defects and there is still room for sorting out the essential mechanisms of binding; iii) RNA binding and DNA binding appear to follow similar driving forces and iv) dataset bias may exist in some methods.     

Parallel and nonparallel behavioural evolution in response to parasitism and predation in Trinidadian guppies

Natural enemies such as predators and parasites are known to shape intraspecific variability of behaviour and personality in natural populations, yet several key questions remain: (i) What is the relative importance of predation vs. parasitism in shaping intraspecific variation of behaviour across generations? (ii) What are the contributions of genetic and plastic effects to this behavioural divergence? (iii) And to what extent are responses to predation and parasitism repeatable across independent evolutionary lineages? We addressed these questions using Trinidadian guppies (Poecilia reticulata) (i) varying in their exposure to dangerous fish predators and Gyrodactylus ectoparasites for (ii) both wild‐caught F0 and laboratory‐reared F2 individuals and coming from (iii) multiple independent evolutionary lineages (i.e. independent drainages). Several key findings emerged. First, a population's history of predation and parasitism influenced behavioural profiles, but to different extent depending on the behaviour considered (activity, shoaling or boldness). Second, we had evidence for some genetic effects of predation regime on behaviour, with differences in activity of F2 laboratory‐reared individuals, but not for parasitism, which had only plastic effects on the boldness of wild‐caught F0 individuals. Third, the two lineages showed a mixture of parallel and nonparallel responses to predation/parasitism, with parallel responses being stronger for predation than for parasitism and for activity and boldness than for shoaling. These findings suggest that different sets of behaviours provide different pay‐offs in alternative predation/parasitism environments and that parasitism has more transient effects in shaping intraspecific variation of behaviour than does predation.     

The evolution of eyes and visually guided behaviour

The morphology and molecular mechanisms of animal photoreceptor cells and eyes reveal a complex pattern of duplications and co-option of genetic modules, leading to a number of different light-sensitive systems that share many components, in which clear-cut homologies are rare. On the basis of molecular and morphological findings, I discuss the functional requirements for vision and how these have constrained the evolution of eyes. The fact that natural selection on eyes acts through the consequences of visually guided behaviour leads to a concept of task-punctuated evolution, where sensory systems evolve by a sequential acquisition of sensory tasks. I identify four key innovations that, one after the other, paved the way for the evolution of efficient eyes. These innovations are (i) efficient photopigments, (ii) directionality through screening pigment, (iii) photoreceptor membrane folding, and (iv) focusing optics. A corresponding evolutionary sequence is suggested, starting at non-directional monitoring of ambient luminance and leading to comparisons of luminances within a scene, first by a scanning mode and later by parallel spatial channels in imaging eyes.     

Gene networks capable of pattern formation: from induction to reaction-diffusion

One of the main aims of developmental biology is to understand how a single and apparently homogeneous egg cell achieves the intricate complexity of the adult. Here we present two models to explain the generation of developmental patterns through interactions at the gene level. One model considers direct-contact induction between cells while the other takes into account diffusion of hormones. We show that sets of cells involving identical gene networks and communicating through hormones spontaneously exhibit ordered patterns. We have characterized these patterns and the specific networks responsible for them. The models allow to (i) compare diffusion and direct-contact induction processes as mechanisms of pattern generation; (ii) identify the possible range of behaviour of real gene networks and (iii) suggest causal mechanisms to generate known patterns. The evolutionary implications are discussed.     

The biological activity of 4-chloromethylbiphenyl, benzyl chloride and 4-hydroxymethylbiphenyl in 4 short-term tests for carcinogenicity. A report of an individual study in the UKEMS genotoxicity trial 1981

4-Chloromethylbiphenyl (4CMB), benzyl chloride (BC) and 4-hydroxymethyl-biphenyl (4HMB) were tested for biological activity in the following assays: (i) the Salmonella/microsome assay; (ii) a bacterial 'fluctuation' assays; (iii) a DNA repair assay in Hela cells, and (iv) a mouse lymphoma mutation assay. 4CMB was active in assays (i), (ii) and (iii) but not in (iv); BC was active in assays (i), (ii), (iii) but not in (iv) while 4HMB was inactive in all assays. Where biological activity was seen this did not require addition of a liver S9 preparation. 4CMB was more active than BC in all the test systems in which a positive response was obtained. The implication of these results for a test battery approach to in vitro testing is discussed.     

The biological activity of 4-chloromethylbiphenyl,benzyl chloride and 4-hydroxymethylbiphenyl in 4 short-term tests for carcinogenicity: A report of an individual study in the UKEMS genotoxity trial 1981

4-Chloromethylbiphenyl (4CMB), benzyl chloride (BC) and 4-hydroxymethyl-biphenyl (4HMB) were tested for biological activity in the following assays: (i) the Salmonella/microsome assay; (ii) a bacterial ‘fluctuation’ assays; (iii) a DNA repair assay in Hela cells, and (iv) a mouse lymphoma mutation assay. 4CMB was active in assays (i), (ii) and (iii) but not in (iv); BC was active in assays (i), (ii), (iii) but not in (iv) while 4HMB was inactive in all assays. Where biological activity was seen this did not require addition of a liver S9 preparation. 4CMB was more active than BC in all the test systems in which a positive response was obtained. The implication of these results for a test battery approach to in vitro testing is discussed.     

Footprinting with an automated capillary DNA sequencer

Footprinting is a valuable tool for studying DNA-protein contacts. However, it usually involves expensive, tedious and hazardous steps such as radioactive labeling and analyses on polyacrylamide sequencing gels. We have developed an easy four-step footprinting method involving (i) the generation and purification of a PCR fragment that is fluorescently labeled at one end with 6-carboxyfluorescein; (ii) brief exposure of the fragment to a DNA-binding protein and then DNase I; (iii) spin-column purification; and (iv) analysis of partial digestion products on the ABI Prism 310 capillary DNA sequencer/genetic analyzer. Very detailed and sensitive footprints of large (> 400 bp) DNA fragments can be easily obtained, as illustrated by our use of this method to characterize binding of PhcA, a LysR-type activator, to two sites greater than 100 bp apart in the 5' untranslated region of xpsR, one of its regulated target genes. The advantages of this new method are that it (i) uses long-lived, safe and easy-to-make fluorescently labeled target fragments; (ii) uses sensitive, robust and highly reproducible fragment analysis using an automated DNA sequencer, instead of gel electrophoresis and autoradiography; and (iii) is cost effective.