The Biology of Time and Death

The steady flow of solar energy through prebiotic chemical systems forced them to undergo material cycles, and this cycling was inherited by living organisms. Organisms whose cycling synchronized with periodic phenomena, such as day/night and seasonal variations were favored. At a later stage, evolution also favored organisms that, besides of a synchronized cycling, developed a ‘sense of time’ to cope with non-cyclic and unique events in the environment. In the case of human beings, this ‘sense of time’ was used to detect causal chains (cause → effect), combine them to produce dynamic models of reality, and transform real time scales into mental time scales (it takes a moment to remember a year-long phenomenon). The ‘sense of time’ constituted a decisive evolutive advantage, because it enables humans to analyze a multitude of future possibilities, and choose the most promising one. Yet ‘sense of time’ is just an empty metaphore, because it is not a true ‘sense’, and we ignore what ‘time’ really is. Most scientific disciplines simply take for granted that there is a ‘time flowing from future to past’. Biologists instead, cannot adopt this attitude because ‘time’ may very well be an intrinsic property of our mind, i.e., a peculiar aspect of brain physiology.     

Perspective: Time scales in scientific research with an emphasis on microbial cellular and molecular research

Scientists use time to describe and research the universe in which humans live. Geologists and evolutionary biologists often use time scales in the millions to billions of years while biochemists and molecular biologists use time scales in the milliseconds or less. The atom smashers use time scales that are almost the speed of light. However, in some areas of research such as molecular-based activities in cells, it is very challenging to obtain data sets in molecular time scales. This has been a challenge to obtaining accurate and precise measurements at the cell and molecular levels of organization in living organisms. Measurements of specific cellular and molecular activities are often made over time scales longer than the actual molecular events. The data sets obtained become estimates over seconds, minutes and hours and not measurements over milli- and nanoseconds. The question can then be posed — how representative and accurate are our data sets when the time scales are not synchronized with the actual living events? In this article, the role of time scales in scientific research and our understanding of living microorganisms are examined with an emphasis on cell and molecular time scales.     

General Rules for Optimal Codon Choice

Different synonymous codons are favored by natural selection for translation efficiency and accuracy in different organisms. The rules governing the identities of favored codons in different organisms remain obscure. In fact, it is not known whether such rules exist or whether favored codons are chosen randomly in evolution in a process akin to a series of frozen accidents. Here, we study this question by identifying for the first time the favored codons in 675 bacteria, 52 archea, and 10 fungi. We use a number of tests to show that the identified codons are indeed likely to be favored and find that across all studied organisms the identity of favored codons tracks the GC content of the genomes. Once the effect of the genomic GC content on selectively favored codon choice is taken into account, additional universal amino acid specific rules governing the identity of favored codons become apparent. Our results provide for the first time a clear set of rules governing the evolution of selectively favored codon usage. Based on these results, we describe a putative scenario for how evolutionary shifts in the identity of selectively favored codons can occur without even temporary weakening of natural selection for codon bias.     

Courting disaster: How diversification rate affects fitness under risk

Life is full of risk. To deal with this uncertainty, many organisms have evolved bet-hedging strategies that spread risk through phenotypic diversification. These rates of diversification can vary by orders of magnitude in different species. Here we examine how key characteristics of risk and organismal ecology affect the fitness consequences of variation in diversification rate. We find that rapid diversification is strongly favored when the risk faced has a wide spatial extent, with a single disaster affecting a large fraction of the population. This advantage is especially great in small populations subject to frequent disaster. In contrast, when risk is correlated through time, slow diversification is favored because it allows adaptive tracking of disasters that tend to occur in series. Naturally evolved diversification mechanisms in diverse organisms facing a broad array of environmental risks largely support these results. The theory presented in this article provides a testable ecological hypothesis to explain the prevalence of slow stochastic switching among microbes and rapid, within-clutch diversification strategies among plants and animals.     

Effect of Hawk-Dove Game on the Dynamics of Two Competing Species

Outcomes of interspecific competition, and especially the possibility of coexistence, have been extensively studied in theoretical ecology because of their implications in community assemblages. During the last decades, the influence of different time scales through the local/regional dynamics of animal communities has received an increasing attention. Nevertheless, different time scales involved in interspecific competition can result form other processes than spatial dynamics. Here, we envision and analyze a new theoretical framework that couples a game theory approach for competition with a demographic model. We take advantage of these two time scales to derive a reduced model governing the total densities of the two populations and we study how these two time scales interfere and influence outcomes of species competition. We find that a competition process occurring on a faster time scale than demography yields a “priority effect” where the first species introduced outcompetes the other one. We then confirm previous findings stipulating that species coexistence is favored by large difference in time scales because the extinction/recolonization process. Our results then highlight that an integration of demographic and competition time scales at both local and regional levels is mandatory to explain communities assemblages and should become a research priority.     

A hierarchical approach to evaluating the significance of soil biodiversity to biogeochemical cycling

The significance of biodiversity to biogeochemical cycling is viewed most directly through the specific biogeochemical transformations that organisms perform. Although functional diversity in soils can be great, it is exceeded to a high degree by the richness of soil species. It is generally inferred from this richness that soil systems have a high level of functional redundancy. As such, indices of species richness probably contribute little to understanding the functioning of soil ecosystems. Another approach stresses the value of identifying keystone organisms, that is those that play an exceptionally important role in determining the structure and function of ecosystems. Both views tend to ignore the importance of biodiversity in maintaining the numerous and complex interactions among organisms in soils and their contributions to biogeochemical cycling. We describe some of those interactions and their importance to ecosystem function.Soil organisms alter the physical, chemical and biological properties of soils in innumerable ways. The composition and structure of biotic communities at one hierarchical level can influence the spatial heterogeneity of resource and refuge patches at other hierarchical levels. This spatial heterogeneity is supported by a number of biologically relevant spheres of influence that include the detritusphere, the drilosphere, the porosphere, the aggregatusphere and the rhizosphere. Each has fairly distinct properties that operate at different spatial scales. We discuss how these properties may function in regulating the interactions among organisms and the biogeochemical processes that they mediate. It is through the formation of a spatially and temporally heterogeneous structure that biodiversity may contribute most significantly to the functioning of soil ecosystems. Real advances in understanding the significance of biodiversity to biogeochemical cycling will come from taking a broader view of biodiversity. Such a view will necessarily encompass many levels of resolution including: 1) the importance of biodiversity to specific biogenic transformations, 2) the complexity and specificity of biotic interactions in soils that regulate biogeochemical cycling, and 3) how biodiversity may operate at different hierarchically arranged spatial and temporal scales to influence the structure and function of ecosystems.     

Human dissemination of genes and microorganisms in Earth's Critical Zone

Earth's Critical Zone sustains terrestrial life and consists of the thin planetary surface layer between unaltered rock and the atmospheric boundary. Within this zone, flows of energy and materials are mediated by physical processes and by the actions of diverse organisms. Human activities significantly influence these physical and biological processes, affecting the atmosphere, shallow lithosphere, hydrosphere, and biosphere. The role of organisms includes an additional class of biogeochemical cycling, this being the flow and transformation of genetic information. This is particularly the case for the microorganisms that govern carbon and nitrogen cycling. These biological processes are mediated by the expression of functional genes and their translation into enzymes that catalyze geochemical reactions. Understanding human effects on microbial activity, fitness and distribution is an important component of Critical Zone science, but is highly challenging to investigate across the enormous physical scales of impact ranging from individual organisms to the planet. One arena where this might be tractable is by studying the dynamics and dissemination of genes for antibiotic resistance and the organisms that carry such genes. Here we explore the transport and transformation of microbial genes and cells through Earth's Critical Zone. We do so by examining the origins and rise of antibiotic resistance genes, their subsequent dissemination, and the ongoing colonization of diverse ecosystems by resistant organisms.     

To be or not to be rhythmic? A review of studies on organisms inhabiting constant environments

Abstract

Circadian clocks are endogenous time keeping mechanisms that drive near 24-h behavioural, physiological and metabolic rhythms in organisms. It is thought that organisms possess circadian clocks to facilitate coordination of essential biological events to the external day and night (extrinsic advantage) so as to enhance Darwinian fitness. However, on Earth, there are a number of habitats that are not subject to such robust daily cycling of geo-physical factors. Do organisms living under such conditions exhibit rhythmic behaviours that are driven by endogenous circadian clocks? We attempt to critically survey studies of rhythms (or the lack of them) in organisms living in a range of constant environments. Many such organisms do show rhythms in behaviour and/or physiological variables. We suggest that such presence of rhythms may be indicative of an underlying clock that facilitates, (a) internal synchrony among rhythms, and (b) temporal partitioning of incompatible cellular processes (intrinsic advantage). We then highlight reasons that limit our interpretations about the presence (or absence) of clocks in such organisms living under constant conditions, and suggest possible methods to conclusively test whether or not rhythms in these organisms are driven by endogenous circadian clocks with the hope that it may enhance our understanding of circadian clocks in organisms under constant environments.     

Experimental studies of evolution in guppies: a model for understanding the evolutionary consequences of predator removal in natural communities

Guppies (Poecilia reticulata) in Trinidadian streams are found with a diversity of predators in the lower reaches of streams, but few predators in the headwaters. These differences have caused the adaptive evolution of guppy behaviour, morphology, male colouration and life history. Waterfalls often serve as barriers to the upstream distribution of predators and/or guppies. Such discontinuities make it possible to treat streams like giant test tubes by introducing guppies or predators to small segments of streams from which they were previously excluded. Such experiments enable us to document how fast evolution can occur and the fine spatial scales over which adaptation is possible. They also demonstrate that the role predators play in structuring this ecosystem resembles many others studied from a more purely ecological perspective; in these streams, as elsewhere, predators depress the numbers of individuals in prey species which in turn reduces the effects of the prey species on other trophic levels and hence the structure of the ecosystem. A focus on predators is important in conservation biology because predators are often the organisms that are most susceptible to local extinction. Their selective loss occurs because large predators have been deliberately exterminated and/or are more susceptible to environmental disturbances. Furthermore, we will argue that predator re-introductions might be destabilizing if, in the absence of predators, their prey have evolved in a fashion that makes them highly susceptible to predation, even after time intervals as short as 50-100 years. A better understanding of the evolutionary impacts of top predators will be critical goal for the policy and practice of large carnivore restoration in the future.     

Recombinant entomopathogenic agents: a review of biotechnological approaches to pest insect control

Although the use of chemical pesticides has decreased in recent years, it is still a common method of pest control. However, chemical use leads to challenging problems. The harm caused by these chemicals and the length of time that they will remain in the environment is of great concern to the future and safety of humans. Therefore, developing new pest control agents that are safer and environmentally compatible, as well as assuring their widespread use is important. Entomopathogenic agents are microorganisms that play an important role in the biological control of pest insects and are eco-friendly alternatives to chemical control. They consist of viruses (non-cellular organisms), bacteria (prokaryotic organisms), fungi and protists (eukaryotic organisms), and nematodes (multicellular organisms). Genetic modification (recombinant technology) provides potential new methods for developing entomopathogens to manage pests. In this review, we focus on the important roles of recombinant entomopathogens in terms of pest insect control, placing them into perspective with other views to discuss, examine and evaluate the use of entomopathogenic agents in biological control.     

Effects of soil nitrogen on diploid advantage in fireweed,Chamerion angustifolium (Onagraceae)

In many ecosystems, plant growth and reproduction are nitrogen limited. Current and predicted increases of global reactive nitrogen could alter the ecological and evolutionary trajectories of plant populations. Nitrogen is a major component of nucleic acids and cell structures, and it has been predicted that organisms with larger genomes should require more nitrogen for growth and reproduction and be more negatively affected by nitrogen scarcities than organisms with smaller genomes. In a greenhouse experiment, we tested this hypothesis by examining whether the amount of soil nitrogen supplied differentially influenced the performance (fitness, growth, and resource allocation strategies) of diploid and autotetraploid fireweed (Chamerion angustifolium). We found that soil nitrogen levels differentially impacted cytotype performance, and in general, diploids were favored under low nitrogen conditions, but this diploid advantage disappeared under nitrogen enrichment. Specifically, when nitrogen was scarce, diploids produced more seeds and allocated more biomass toward seed production relative to investment in plant biomass or total plant nitrogen than did tetraploids. As nitrogen supplied increased, such discrepancies between cytotypes disappeared. We also found that cytotype resource allocation strategies were differentially dependent on soil nitrogen, and that whereas diploids adopted resource allocation strategies that favored current season reproduction when nitrogen was limiting and future reproduction when nitrogen was more plentiful, tetraploids adopted resource allocation strategies that favored current season reproduction under nitrogen enrichment. Together these results suggest nitrogen enrichment could differentially affect cytotype performance, which could have implications for cytotypes’ ecological and evolutionary dynamics under a globally changing climate.     

Long-term climate forcing in loggerhead sea turtle nesting

The long-term variability of marine turtle populations remains poorly understood, limiting science and management. Here we use basin-scale climate indices and regional surface temperatures to estimate loggerhead sea turtle (Caretta caretta) nesting at a variety of spatial and temporal scales. Borrowing from fisheries research, our models investigate how oceanographic processes influence juvenile recruitment and regulate population dynamics. This novel approach finds local populations in the North Pacific and Northwest Atlantic are regionally synchronized and strongly correlated to ocean conditions--such that climate models alone explain up to 88% of the observed changes over the past several decades. In addition to its performance, climate-based modeling also provides mechanistic forecasts of historical and future population changes. Hindcasts in both regions indicate climatic conditions may have been a factor in recent declines, but future forecasts are mixed. Available climatic data suggests the Pacific population will be significantly reduced by 2040, but indicates the Atlantic population may increase substantially. These results do not exonerate anthropogenic impacts, but highlight the significance of bottom-up oceanographic processes to marine organisms. Future studies should consider environmental baselines in assessments of marine turtle population variability and persistence.     

Diversity of Species and Interactions in the Upper Tree Canopy of Forest Ecosystems

SYNOPSIS. The importance of the organisms and processes thatoccur in forest canopies is becoming increasingly recognizedin relation to understanding biodiversity. The upper tree canopyof many forest ecosystems fosters extremely diverse communities,particularly of vascular epiphytes and arthropods. Epiphytesalso contribute to the diversity of birds because they add tothe total amounts of resources, provide opportunities for resourcespecialization, and temporally spread available resources inthe canopy throughout the year. Epiphytes also contribute toecosystem processes such as nutrient cycling because they gainaccess to nutrient sources originating outside the ecosystemand transfer them to other members of the forest, thus functioningas a "keystone" resource.     

Global Climate Change: Benefit-Cost Analysis vs. the Precautionary Principle

The precautionary principle appears to be directly applicable to the prospect that human activities will cause substantial changes to global climate. The magnitude and characteristics of the change in climate and its effects on human activities and unmanaged ecosystems are highly uncertain, potentially catastrophic, and nearly irreversible on human time scales. Nevertheless, the precautionary principle adds little to benefit cost analysis for evaluating climate policies. Benefit cost analysis can incorporate aversion to uncertainty about future outcomes, and also provides a method for balancing this concern against concern for uncertain near term policy costs. The policies favored by setting constraints on future outcomes, such as atmospheric stabilization and tolerable windows, may be less precautionary than the policies favored by benefit cost analysis, as benefit cost analysis can more readily accommodate concerns for moderate as well as severe harms. Concerns about possible climate catastrophes can also be incorporated in benefit cost analysis and, in any event, may have limited implications for policy choice.     

Microbial diversity of cellulose hydrolysis

Enzymatic hydrolysis of cellulose by microorganisms is a key step in the global carbon cycle. Despite its abundance only a small percentage of microorganisms can degrade cellulose, probably because it is present in recalcitrant cell walls. There are at least five distinct mechanisms used by different microorganisms to degrade cellulose all of which involve cellulases. Cellulolytic organisms and cellulases are extremely diverse possibly because their natural substrates, plant cell walls, are very diverse. At this time the microbial ecology of cellulose degradation in any environment is still not clearly understood even though there is a great deal of information available about the bovine rumen. Two major problems that limit our understanding of this area are the vast diversity of organisms present in most cellulose degrading environments and the inability to culture most of them.     

Time course of the effects of static stretching on cycling economy

Stretching has been implemented as part of the warm-up before physical events and widely thought to promote increased sport performance and decreased injury risk. However, recent research has concluded that static stretching before many exercises inhibits acute power, strength, and sprinting performance. There is little research examining the time course of these effects on moderate intensity cycling. The purpose of this study was to examine the time course of static stretching on cycling economy. The subjects consisted of 5 men and 5 women highly trained endurance cyclists. The first of 3 visits was baseline testing of their cycling VO2max. The second and third visits were either stretching or no stretching before a 30-minute stationary ride at 65% of their VO2max. The stretching condition consisted of four 30-second repetitions of 5 stretches with an average total stretching time of 16 minutes. VO2 demonstrated a significant condition by time interaction with the 5-minute time point being significantly less in the nonstretching condition (32.66 ± 5.35 ml·kg(-1)·min(-1)) than stretching (34.39 ± 5.39 ml·kg(-1)·min(-1)). No other time points were different. Our results demonstrate that static stretching yielded an acute increase in submaximal VO2; therefore, coaches and highly trained endurance cyclists should exclude static stretching immediately before moderate intensity cycling because it reduces acute cycling economy.     

Environmental change and carbon limitation in trees: a biochemical, ecophysiological and ecosystem appraisal

As C(3) photosynthesis is not yet CO(2)-saturated, forests offer the possibility of enhanced growth and carbon (C) sequestration with rising atmospheric CO(2). However, at an ecosystem scale, increased photosynthetic rates are not always translated into faster tree growth, and in free air carbon enrichment (FACE) experiments with trees, the stimulation in above-ground growth often declines with time. So is tree growth C-limited? The evidence is reviewed here at three different scales. First, at the biochemical scale, the role of Rubisco is discussed by considering its evolution and role as a nitrogen (N) storage protein. Second, at the ecophysiological scale, C allocation to gain nutrients from the soil is considered and it is argued that any C limitation is only through a limitation to soil nutrient cycling. Finally, the response of forest ecosystems to rising atmospheric CO(2) concentrations is considered and evidence from FACE experiments is discussed. From the three lines of evidence we conclude that the growth of trees is not C-limited, with the key to understanding future responses to climate change being turnover of soil organic matter and nutrient cycling.     

Contrasting spatial heterogeneity of sessile organisms within mussel (Perna perna L.) beds in relation to topographic variability

We examined the spatial heterogeneity in three sessile rocky shore organisms, the mussel Perna perna, the barnacle Octomeris angulosa (Sowerby) and the red alga Gelidium pristoides (Turn.) at a range of continuous local scales along horizontal transects within mid- and upper mussel beds of South African shores. We also examined the relationships between variability of organisms and topographic features (rock depressions, slope, aspect), and between mussel, barnacle and algal variability over the same scales. To estimate spatial heterogeneity, we analyzed scaling properties of semivariograms using a fractal approach. Relationships between different variables at the different scales were examined by cross-semivariograms. Spatial dependence of P. perna variability increased with spatial dependence of topographic variability, so that scaling regions of mussel and topographic distributions corresponded well. This relationship often improved with larger local scales (mussel cover increased with depressions, steeper slope and aspect towards waves), while at smaller spatial scales, variability in mussel cover was less well explained by variability in topography. The variability of the barnacle O. angulosa exhibited spatial dependence, even on topographically unstructured shores. In contrast, the distribution of the alga G. pristoides revealed high fractal dimensions, showing spatial independence on topographically unstructured shores. Algae also showed a very strong negative relationship with mussels at most local scales, and a negative relationship with barnacles in upper zones, especially at larger local scales. Barnacles may show clear spatial dependence because of hydrodynamics (at larger local scales) and the need to find a future mate in close proximity (at smaller local scales), while algae may show a strong negative relationship with mussels because of competition for space.