Quantitative analysis of electroencephalograms: is there chaos in the future?

The history of quantitative, computerized electroencephalogram (EEG) analysis is reviewed. It is shown that, until very recently, the basic approach to EEG analysis involved the assumption that the EEG is stochastic. Consequently, statistical pattern recognition techniques, segmentation procedures, syntactic methods, knowledge-based approaches, and even artificial neural network methods have been developed with different levels of success. A fundamentally different approach to computerized EEG analysis, however, is making its way into the laboratories. The basic idea, inspired by recent advances in the area of non-linear dynamics, and especially the theory of chaos, is to view an EEG as the output of a deterministic system of relatively simple complexity, but containing non-linearities. This suggests that studying the geometrical dynamics of EEGs, and the development of neurophysiologically realistic models of EEG generation may produce more successful automated EEG analysis techniques than the classical, stochastic methods. Evidence supporting the non-linear dynamics paradigm is reviewed, and possible research paths are indicated.     

Is there chaos in plankton dynamics?

A controversial issue in ecosystem modeling is whether the irregularfluctuations that one observes in nature are due solely to randomenvironmental factors or whether, at least partially, a deterministicmechanism is responsible for the unpredictable behavior. Thissecond alternative is called deterministic chaos and the issuein this paper is to decide if actual plankton time series canvindicate the hypothesis of chaotic dynamics. The near-neighborforecasting method is a recent technique for detecting determinismin a time series and we apply it to measurements of phytoplanktonand zooplankton biomass obtained at a single station in theMiddle Atlantic Bight. Although the results do not concludethe presence of chaos, they do give some support to the ideathat deterministic non-linear trophic dynamics may account forat least some of the variability that is seen in the data, particularlyin terms of inferring zooplankton oscillations from those ofphytoplankton.     

Death by necrosis: Uncontrollable catastrophe,or is there order behind the chaos?

Cells suffer necrotic death when exposed to extreme environmental conditions, adverse and excessive stimuli, or when deleterious mutations are encoded in their genetic material. Unlike apoptosis, which involves a highly regulated and elaborate network of biochemical events and cascades, necrosis has been considered generally to be a chaotic decadence process that effects the inexorable demise of cells otherwise not destined to die. This grim prospect is now slowly being overturned, mostly by exciting new findings in two simple model organisms, Caenorhabditis elegans and Drosophila melanogaster. Despite the wide spectrum of necrosis-initiating conditions, evidence is accumulating that execution of necrotic or neurodegenerative cell death may be carried out by a finite common set of mechanisms.     

Detail in network models of epidemiology: are we there yet?

Network models of infectious disease epidemiology can potentially provide insight into how to tailor control strategies for specific regions, but only if the network adequately reflects the structure of the region's contact network. Typically, the network is produced by models that incorporate details about human interactions. Each detail added renders the models more complicated and more difficult to calibrate, but also more faithful to the actual contact network structure. We propose a statistical test to determine when sufficient detail has been added to the models and demonstrate its application to the models used to create a synthetic population and contact network for the USA.     

Phylogenetic Analysis: How Old are the Parts of Your Body?

According to the National Academy of Sciences, biology students in the USA are not being adequately prepared for successful futures. Of paramount concern is a lack of sufficient training in quantitative and computational skills, which are needed to compete effectively for an array of educational and occupational opportunities. In this paper, we introduce a classroom exercise that invites students to solve a simple biological problem and illustrates the need for a computer-assisted strategy to arrive at a solution. The exercise invites students to consider the question “How old are the parts of your body?” Some features of the human body are more ancient than others. For example, our bodies have both hair and backbones, but backbones arose much earlier in evolutionary history. Our exercise relies upon MEGA 4.0, a free, visually appealing, and intuitive computer program that allows students to gather DNA or protein sequences from electronic databases, then use them to infer phylogenetic trees. Student-inferred phylogenies are used to explore the relative order in which diverse aspects of the human form evolved. In the process, students are trained to use powerful features of MEGA and encouraged through group discussion to consider additional applications of the technology they have learned. Our lesson plan includes a brief video, a web site with essential terminology and links for further exploration, a hands-on experience using MEGA, and a follow-up discussion.     

How many fold types of protein are there in nature?

Many protein structures have now been determined and reveal that protein molecules can adopt the same fold despite having very different sequences. It has been suggested that, owing to different stereochemical constraints, the number of ways that a sequence can fold may be limited. Therefore, it is reasonable to ask how many fold types exist in nature. Several groups have tackled this problem with very different results. In the present study, a novel statistical sampling approach is used to reestimate this number. The results suggest that the number of protein folds in nature is probably several hundreds. © 1996 Wiley-Liss, Inc.     

Dissemination of spores in a glasshouse: Pattern or chaos?

The dissemination of particles in a glasshouse with three united compartments was observed from experiments withLycopodium sp. The experiments were performed in a glasshouse with open and closed ventilation openings, spore sources on two heights above soil surface, and in two consecutive time intervals. The spores were caught with self constructed spore traps placed at regular distances from each other. Air circulation was observed using smoke-puffs. High ventilation caused a rapid cleaning of the air while in a closed glasshouse spores remained suspended for quite a long time. Though the three compartments of the glasshouse were not separated by walls, a so-called cell structure of the individual compartments could be indicated.     

Stem cell dynamics in Cnidaria: are there unifying principles?

The study of stem cells in cnidarians has a history spanning hundreds of years, but it has primarily focused on the hydrozoan genus Hydra. While Hydra has a number of self-renewing cell types that act much like stem cells—in particular the interstitial cell line—finding cellular homologues outside of the Hydrozoa has been complicated by the morphological simplicity of stem cells and inconclusive gene expression data. In non-hydrozoan cnidarians, an enigmatic cell type known as the amoebocyte might play a similar role to interstitial cells, but there is little evidence that I-cells and amoebocytes are homologous. Instead, self-renewal and transdifferentiation of epithelial cells was probably more important to ancestral cnidarian development than any undifferentiated cell lineage, and only later in evolution did one or more cell types come under the regulation of a “stem” cell line. Ultimately, this hypothesis and competing ones will need to be tested by expanding genetic and developmental studies on a variety of cnidarian model systems.     

Sexual dimorphism in birds: why are there so many different forms of dimorphism?

Variation in the extent of sexual dimorphism among bird species is traditionally attributed to differences in social mating system. However, there are many different forms of dimorphism among birds, and not all of them show an obvious correlation with social mating system. For example, recent work has shown that many highly polygamous species are, in fact, monomorphic, whereas many putatively monogamous species are dimorphic. In this paper we break up sexual dimorphism into subcomponents and then use comparative analyses to examine the pattern of covariation between these subcomponents and various aspects of sexual, social, and parental behaviour. Our first finding is that size dimorphism and plumage-colour dimorphism do not show the same pattern of covariation. Differences in size dimorphism are associated with variation in social mating system and sex differences in parental care, whereas differences in plumage-colour dimorphism are associated with variation in the frequency of extra-bond paternity. These results suggest that size dimorphism is associated with the sort of intrasexual competition described by traditional classifications of social mating system, whereas plumage-colour dimorphism is associated with cryptic female choice. However, when we break up plumage-colour dimorphism according to whether it is due to melanins, carotenoids or structural colours, we find that each category of plumage-colour dimorphism shows a different pattern of covariation. The correlation between overall plumage-colour dimorphism and the rate of extra-bond paternity is due to structural colours, whereas melanin-based dimorphism is associated with sex differences in parental care. The former result is particularly interesting given that new work suggests structural colours are associated with active sexual displays and the reflection of ultraviolet light.     

Pharmacogenetic studies of epilepsy drugs: are we there yet?

One of the mantras of scientists working in the field of pharmacogenetics is 'the right dose for the right patient'. A recent article has gone someway towards demonstrating that this goal can be achieved using genetic approaches. It is one of the first reports to show that a specific polymorphism can predict the maximum tolerated dose of two anti-epileptic drugs. However, further studies are necessary to validate these observations.     

Is there chaos in the brain? I. Concepts of nonlinear dynamics and methods of investigation

In the light of results obtained during the last two decades in a number of laboratories, it appears that some of the tools of nonlinear dynamics, first developed and improved for the physical sciences and engineering, are well-suited for studies of biological phenomena. In particular it has become clear that the different regimes of activities undergone by nerve cells, neural assemblies and behavioural patterns, the linkage between them, and their modifications over time, cannot be fully understood in the context of even integrative physiology, without using these new techniques. This report, which is the first of two related papers, is aimed at introducing the non expert to the fundamental aspects of nonlinear dynamics, the most spectacular aspect of which is chaos theory. After a general history and definition of chaos the principles of analysis of time series in phase space and the general properties of chaotic trajectories will be described as will be the classical measures which allow a process to be classified as chaotic in ideal systems and models. We will then proceed to show how these methods need to be adapted for handling experimental time series; the dangers and pitfalls faced when dealing with non stationary and often noisy data will be stressed, and specific criteria for suspecting determinism in neuronal cells and/or assemblies will be described. We will finally address two fundamental questions, namely i) whether and how can one distinguish, deterministic patterns from stochastic ones, and, ii) what is the advantage of chaos over randomness: we will explain why and how the former can be controlled whereas, notoriously, the latter cannot be tamed. In the second paper of the series, results obtained at the level of single cells and their membrane conductances in real neuronal networks and in the study of higher brain functions, will be critically reviewed. It will be shown that the tools of nonlinear dynamics can be irreplaceable for revealing hidden mechanisms subserving, for example, neuronal synchronization and periodic oscillations. The benefits for the brain of adopting chaotic regimes with their wide range of potential behaviours and their aptitude to quickly react to changing conditions will also be considered.     

Juvenile-adult distribution of the bivalve Mya arenaria on intertidal flats in the Wadden Sea: why are there so few year classes?

Patchy distribution is frequently observed in benthic marine invertebrates. In order to indentify factors causing spatial patterns in the bivalve Mya arenaria, abundances of juveniles and adults, as well as death assemblages, were recorded on a 20-km scale in the intertidal zone of the Sylt-Rømø Bight. Both adults and juveniles exhibited pronounced patchiness. Shell length of juveniles rarely exceeded 2 mm in 1995, which was most likely a consequence of epibenthic predators truncating the size spectrum. Only a few yearclasses dominated the adult population. While the northern part of the Bight was colonized mainly by a 1993-cohort, most M. arenaria in the southern part were from the mid-1980s. It is hypothesized that epibenthic predation is a major cause of the lack of dense M. arenaria beds from other years. However, examination of the length–frequency distribution of death assemblages revealed that other unidentified causes of mortality exist. High abundances of adults were found in the mid and lower intertidal zone but not in the high intertidal zone. There was no indication that dispersal of M. arenaria spat in a landward or seaward direction contributed significantly to the observed distribution pattern, since spat occurred abundantly at all tidal levels except in the high intertidal zone. There was no evidence of negative adult-juvenile interaction. M. arenaria was not attracted by seagrass or projecting shell beds – the latter indicating erosion of the sediment – as abundances of adults and juveniles were generally low in these habitats. The effects of sediment type and of the bioturbating lugworm Arenicola marina were inconsistent. While adults were more abundant on muddy sand than on sand, recruitment was independent of sediment type. At all high density sites of adults (>50 ind m^–2), lugworm densities were below 5 ind m^–2, which may indicate a negative interaction. However, lugworm densities >30 ind m^–2 did not prevent relatively high M. arenaria recruitment of >500 ind m^–2.     

How many species of cichlid fishes are there in African lakes?

The endemic cichlid fishes of Lakes Malawi, Tanganyika and Victoria are textbook examples of explosive speciation and adaptive radiation, and their study promises to yield important insights into these processes. Accurate estimates of species richness of lineages in these lakes, and elsewhere, will be a necessary prerequisite for a thorough comparative analysis of the intrinsic and extrinsic factors influencing rates of diversification. This review presents recent findings on the discoveries of new species and species flocks and critically appraises the relevant evidence on species richness from recent studies of polymorphism and assortative mating, generally using behavioural and molecular methods. Within the haplochromines, the most species-rich lineage, there are few reported cases of postzygotic isolation, and these are generally among allopatric taxa that are likely to have diverged a relatively long time in the past. However, many taxa, including many which occur sympatrically and do not interbreed in nature, produce viable, fertile hybrids. Prezygotic barriers are more important, and persist in laboratory conditions in which environmental factors have been controlled, indicating the primary importance of direct mate preferences. Studies to date indicate that estimates of alpha (within-site) diversity appear to be robust. Although within-species colour polymorphisms are common, these have been taken into account in previous estimates of species richness. However, overall estimates of species richness in Lakes Malawi and Victoria are heavily dependent on the assignation of species status to allopatric populations differing in male colour. Appropriate methods for testing the specific status of allopatric cichlid taxa are reviewed and preliminary results presented.     

How many species of Cladocera are there?

An estimation of the number of taxa within families, genera and local faunas of Cladocera reveals that only c. 129 species (17% of all known species) may be considered as sufficiently well described (valid species), and c. 146 as rather well described (fair species) but needing further study using modern methods of investigation. The status of all other species is vague. The families Chydoridae, Daphniidae and Sididae and genera Diaphanosoma, Daphnia, (including Daphniopsis), Megafenestra, Scapholeberis, Eurycercus, Chydorus, Ephemeroporus and Pleuroxus have been comparatively studied best. The largest number of valid species is known from Europe, North America, Australia and South America, and the smallest number from Africa. Presence of large number of vague species of Cladocera negatively affects faunistic, zoogeographic, and ecological studies of continental waters.Dedicated to the memory of Professor D. J. Frey     

Why are there about 5000 species of phytoplankton in the sea?

The relative abundances of phytoplankton taxa conform approximatelyto a finite geometric series in which there are 20–25species per decade of ranked abundance. Such series can contain160–400 species between the commonest (10²²–10²⁶cells) and the rarest (10¹⁰–10¹⁴ cells). Thus, between12 and 31 such series are needed to explain the observed diversity,5x10³ species, of marine phytoplankton. The number of seriesis similar to the number (20–25) of upper-ocean watermasses defined by dilution time scale of order 10¹–10²years. Interpretations of this coincidence are discussed.     

Characterization of motor patterns in isolated human colon: are there differences in patients with slow-transit constipation?

The patterns of motor activity that exist in isolated full-length human colon have not been described. Our aim was to characterize the spontaneous motor patterns in isolated human colon and determine whether these patterns are different in whole colons obtained from patients with slow-transit constipation (STC). The entire colon (excluding the anus), was removed from patients with confirmed STC and mounted longitudinally in an organ bath ～120 cm in length, containing oxygenated Krebs' solution at 36°C. Changes in circular muscle tension were recorded from multiple sites simultaneously along the length of colon, by use of isometric force transducers. Recordings from isolated colons from non-STC patients revealed cyclical colonic motor complexes (CMCs) in 11 of 17 colons, with a mean interval and half-duration of contractions of 4.0 ± 0.6 min and 51.5 ± 15 s, respectively. In the remaining six colons, spontaneous irregular phasic contractions occurred without CMCs. Interestingly, in STC patients robust CMCs were still recorded, although their CMC pacemaker frequencies were slower. Intraluminal balloon distension of the ascending or descending colon evoked an ascending excitatory reflex contraction, or evoked CMC, in 8 of 30 trials from non-STC (control) colons, but not from colons obtained from STC patients. In many control segments of descending colon, spontaneous CMCs consisted of simultaneous ascending excitatory and descending inhibitory phases. In summary, CMCs can be recorded from isolated human colon, in vitro, but their intrinsic pacemaker frequency is considerably faster in vitro compared with previous human recordings of CMCs in vivo. The observation that CMCs occur in whole colons removed from STC patients suggests that the intrinsic pacemaker mechanisms underlying their generation and propagation are preserved in vitro, despite impaired transit along these same regions in vivo.     

At-sea abundance and spatial distribution of South American sea lion (Otaria byronia) in Chilean Northern Patagonia: How many are there?

The South American sea lion (Otaria byronia) (SSL) is a widespread opportunistic predator that inhabits waters ranging from Southern Ecuador to Southern Chile in the Pacific Ocean and from Southern Brazil to Southern Argentina in the Atlantic. SSL abundance estimates, as for many pinniped species, have relied on shore censuses, with the uncertainty that an indeterminate number of individuals at sea might remain uncounted. The proportion of the population that remains at sea during censuses and their distribution patterns are not clear and has been scarcely assessed. We used line transect sampling to gather information about at-sea abundance, density and spatial distribution of SSL in coastal waters off the Chilean Northern Patagonia. A total of 123 groups were sighted while on-effort, with an estimated density of 0.393 ind./km² (95%CI = 0.262–0.591) and a total abundance, for the surveyed area, of 13,721 individuals (95%CI = 9127–20,627). Even when our survey was rather restricted in spatial range, generalized additive model results showed that depth, distance to SSL rockeries, coastline complexity and geographical coordinates had a significant influence on SSL spatial distribution. The results on abundance and spatial distribution of SSL at sea are discussed in terms of current population estimates. Our substantial at-sea abundance estimate suggests that shore censuses might have been historically biased. Several aspects should be taken into account in further research on SSL abundance, such as including pelagic waters and undertaking simultaneously on-rockery and marine SSL abundance estimates. The results presented here provide valuable insights for revisiting and possibly improve population estimates of SSL and other pinnipeds species worldwide. This is particularly relevant when management and conservation actions need to be taken on those species that have strong interactions with fisheries and aquaculture.