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.     

城市化对流域生态水文过程的影响研究综述

了解流域水文过程(水量和水质)是流域综合管理的基础。城市化引起的生态环境问题已成为目前和未来一段相当长的时期内人类社会面临的重大问题。然而,城市化(土地利用/覆被变化、新污染物产生)、水文(降水、入渗、蒸散、径流过程)和生态系统服务(产水服务、调节气候、土壤保持、初级生产力、维持生物多样性等)在不同时空尺度之间的相互作用还存在知识空白。从城市化对流域生态系统结构和功能的影响、城市化对地表能量平衡与水量平衡的影响、城市化对水质和水生生物的影响、以及城市土地利用/覆被变化的大气环境效应等多方面系统总结了城市化影响流域生态水文过程的研究进展。研究发现,城市"热岛"、"干岛"、暴雨径流引起的城市内涝、水污染等环境现象都与生态水文过程密切相关。强调现代城市规划需要遵循生态水文学规律,从全流域生态系统角度认识近年来新出现的不同尺度的城市环境效应。城市最佳管理措施应以流域为单元实施,以调节土地利用/覆被、保护湿地(包括自然与人工湿地)为手段,充分发挥自然生态系统调节功能(如植被蒸散和净化水质)。未来城市生态水文学应围绕"低影响开发"以及"基于自然的解决方案"等城市流域管理措施,在稳定城市小气候、缓解洪涝干旱等极端水文气象灾害风险以及减轻城市水污染等方面开展多尺度综合研究。     

Where is Darwin 200 years later?

The theory of evolution is perceived by many people, particularly but not only in the United States, as a controversial theory not yet fully demonstrated. Yet, that living organisms, including humans, have evolved from ancestors who were very different from them is beyond reasonable doubt, confirmed by at least as much evidence as any other widely accepted scientific theory. I argue that Darwin’s contribution to science goes much beyond the theory of evolution in itself. The theory of natural selection explains the adaptations of organisms, their ‘design’. The ‘Copernican Revolution’ brought the phenomena of the physical universe into the realm of science: explanations by natural causes that can be tested by observation and experiment. However, the scientific revolution that occurred in the 16th and 17th centuries had left the living world out of scientific explanations, because organisms seemingly show that they are ‘designed,’ and thus call for an intentional designer. It was Darwin’s greatest contribution to science, to demonstrate that the adaptations of organisms, their apparent ‘design’, can be explained by natural processes governed by natural laws. At that point, science came into maturity, because all natural phenomena in the universe, living as well as nonliving, could be investigated scientifically, and explained as matter in motion governed by natural laws.     

From oasis to outlier: sugar beets,an endangered fish,and the moral economy

Farmers in the arid high plains of Eastern Montana had long irrigated with water shunted into their fields by a dam on the Yellowstone River. Growing water-hungry sugar beets processed at a factory in a nearby town, they created a verdant and prosperous oasis: a good life nested within a satisfyingly moral economy. However, in short order, the economic basis of this life was challenged: the dam was threatened with removal because of claims that it adversely affected an endangered fish; and the factory was threatened with closure because of claims that it was insufficiently profitable. As farmers and townsfolk confronted these challenges and the motives of those making them, they were compelled to probe the fundamental questions of what is ‘moral’ and what is ‘economy’. Confronting their uncertain future, they wondered whether their oasis was to become an outlier.     

Do plant communities exist? Evidence from scaling‐up local species‐area relations to the regional level

Abstract. One long tradition in ecology is that discrete communities exist, at least in the sense that there are areas of relatively uniform vegetation, with more rapid change in species composition between them. The alternative extreme view is the Self‐similarity concept – that similar community variation occurs at all spatial scales. We test between these two by calculating species‐area curves within areas of vegetation that are as uniform as can be found, and then extrapolating the within‐community variation to much larger areas, that will contain many ‘communities’. Using the Arrhenius species‐area model, the extrapolations are remarkably close to the observed number of species at the regional/country level. We conclude that the type of heterogeneity that occurs within ‘homogeneous’ communities is sufficient to explain species richness at much larger scales. Therefore, whilst we can speak of ‘communities’ for convenience, the variation that certainly exists at the ‘community’ level can be seen as only a larger‐scale manifestation of micro‐habitat variation.     

Propagule dispersal and the scales of marine community process

Benthic marine organisms are characterized by a bipartite life history in which populations of sedentary adults are connected by oceanic transport of planktonic propagules. In contrast with the terrestrial case, where ‘long distance dispersal’ (LDD) has traditionally been viewed as a process involving rare events, this creates the possibility for large numbers of offspring to travel far relative to the spatial scale of adult populations. As a result, the concept of LDD must be examined carefully when applied in a marine context. Any measure of LDD requires reference to an explicit ‘local’ scale, often defined in terms of adult population demography, habitat patchiness, or the average dispersal distance. Terms such as ‘open’ and ‘closed’ are relative, and should be used with caution, especially when compared across different taxa and systems. We use recently synthesized data on marine propagule dispersal potential and the spread of marine invasive species to draw inferences about average and maximum effective dispersal distances for marine taxa. Foremost, our results indicate that dispersal occurs at a wide range of scales in marine communities. The nonrandom distribution of these scales among community members has implications for marine community dynamics, and for the implementation of marine conservation efforts. Second, in agreement with theoretical results, our data illustrate that average and extreme dispersal scales do not necessarily covary. This further confounds simple classifications of ‘short’ and ‘long’ dispersers, because different ecological processes (e.g. range expansion vs. population replenishment) depend on different aspects of the dispersal pattern (e.g. extremes vs. average). Our findings argue for a more rigorous quantitative view of scale in the study of marine dispersal processes, where relative terms such as ‘short’ and ‘long’, ‘open’ and ‘closed’, ‘retained’ and ‘exported’ are defined only in conjunction with explicit definitions of the scale and process of interest. This shift in perspective represents an important step towards unifying theoretical and empirical studies of dispersal processes in marine and terrestrial systems.     

An overview of river health assessment: philosophies, practice, problems and prognosis

1. Philosophically, the term ‘river health’ is useful because it is readily interpreted by the general public and evokes societal concern about human impacts on rivers. The common goal of achieving healthy rivers unites ecologists and the general public because the value of the ecologists’ contributions is clear (and, hence, funded). The difficulty arises in the choice of relevant symptoms because there is a wide variety that can be measured with varying accuracy at a broad range of spatial scales. These indicators may respond to impacts at different time scales, and no single indicator is a ‘silver bullet’ that reveals river health unequivocally. 2. In practice, choice of indicator often shows personal bias, technical considerations, and constraints of knowledge. Selection of appropriate spatial and temporal scales for these measures is crucial. Although most measurements are spot samples (e.g. concentration, abundance, species richness), assessment of river health based on changes in ecological processes such as post-disturbance recovery rate or nutrient spiralling lengths may be more suitable in some cases. 3. Problems include validation of the indicator, its response time at a range of scales, and the reliability of its measurement. Assessment of river health should be accurate, timely (warning of deterioration instead of waiting until the patient is terminal), rapid (so that the response is swift), and inexpensive. The connectedness of running waters with their floodplains and catchments must be explicitly recognized. Hydrological and geomorphological modifications of rivers usually affect their health by severing or impairing the linkages, and the ‘cure’ may lie in addressing these causes. Often, we need landscape-level data for management because this is the scale where cumulative effects of impacts are evident. 4. The prognosis is uncertain. We need to explore further the use of integrative measures of river health, and focus on establishing a link between the measure and impaired ecological integrity. Ecosystem-level variables (e.g. estimates of production or respiration) show promise and recent technological advances make these more accessible. Data analytical approaches (e.g. multimetric vs. predictive models) need further debate but must not overlook the importance of high quality and relevant input data. Appropriate choice of indicators, rigorous sampling and analysis, and careful data interpretation must be matched with effective communication to policy-makers and the public. When this occurs, the concept of ‘river health’ becomes more than just a rhetorical tool.‘     

The spatial scaling of beta diversity

Beta diversity is an important concept used to describe turnover in species composition across a wide range of spatial and temporal scales, and it underpins much of conservation theory and practice. Although substantial progress has been made in the mathematical and terminological treatment of different measures of beta diversity, there has been little conceptual synthesis of potential scale dependence of beta diversity with increasing spatial grain and geographic extent of sampling. Here, we evaluate different conceptual approaches to the spatial scaling of beta diversity, interpreted from ‘fixed’ and ‘varying’ perspectives of spatial grain and extent. We argue that a ‘sliding window’ perspective, in which spatial grain and extent covary, is an informative way to conceptualize community differentiation across scales. This concept more realistically reflects the varying empirical approaches that researchers adopt in field sampling and the varying scales of landscape perception by different organisms. Scale dependence in beta diversity has broad implications for emerging fields in ecology and biogeography, such as the integration of fine‐resolution ecogenomic data with large‐scale macroecological studies, as well as for guiding appropriate management responses to threats to biodiversity operating at different spatial scales.     

The Age of Angels: spiritualism and evolutionary progressionism in a nineteenth-century geologic time chart

The term ‘Anthropocene’ often carries apocalyptic overtones of environmental devastation, but many nineteenth-century iterations of the ‘Age of Humans’ idea were explicitly optimistic. The current time period was framed as a ‘Psychozoic Era’ or ‘Age of Mind’ in which human beings took their predetermined place at the pinnacle of ‘creation’. Hiram Alvin Reid, an amateur scientist in the midwestern United States, took this line of thinking a step further. He drafted a geologic time chart in which the current ‘Age of Man’ was succeeded by a future ‘Age of Angels’, wherein humans will become higher beings. Reid was a Christian spiritualist who thought that evolution drove both physical and spiritual advancement, including the recent development of a ‘sixth sense’ that allowed humans to perceive ghosts and angels. Reid’s views, while idiosyncratic and coloured by his metaphysical beliefs, drew heavily on mainstream concepts in biology and geology. Prominent geologists like James Dana and Joseph Le Conte argued for an Age of Mind in terms that mixed scientific rigor with religious and progressionist ideas. The Psychozoic was also embraced by many progressive-minded individuals outside the natural sciences, paralleling widespread modern interest in the Anthropocene.     

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.     

Revolución o muerte: Self-Sacrifice and the Ontology of Cuban Revolution

With reference to the experience of the Cuban Revolution, this article addresses what may be called the ‘late revolutionary paradox’: How can so many people in countries such as Cuba continue to pledge visceral allegiance to their revolution while at the same time expressing deep disaffection with it? My main claim is that the paradox is a product of an undue analytical emphasis on the ideological content of revolutionary discourse, with its mantra-like evocations of ‘process’, ‘change’, ‘emancipation’ and other discursive projections into the future. Seen from the point of view of its form as a socio-political event, I argue, revolution turns on a deeper premise, namely the commitment to self-sacrifice, i.e. the assumption that revolutionary subjects are defined by their potential death in defence of the revolution. The premise of self-sacrifice, I argue, lends revolutionary politics a peculiar ontological foundation that makes it radically different to, broadly, ‘liberal’ understandings of politics. This difference, I show, dissolves the putative ‘paradox’ of later revolutionary societies such as Cuba, allowing revolutionary subjects to sustain a sense of revolutionary conviction in the face of the many historical contingencies that would seem otherwise to make such enduring convictions increasingly difficult to sustain.     

Niche construction,adaptive preferences,and the differences between fitness and utility

A number of scholars have recently defended the claim that there is a close connection between the evolutionary biological notion of fitness and the economic notion of utility: both are said to refer to an organism’s success in dealing with its environment, and both are said to play the same theoretical roles in their respective sciences. However, an analysis of two seemingly disparate but in fact structurally related phenomena—‘niche construction’ (the case where organisms change their environment to make it fit to their needs) and ‘adaptive preferences’ (the case where agents change their wants to make them fit to what the world has given them)—shows that one needs to be very careful about the postulation of this sort of fitness–utility connection. Specifically, I here use the analysis of these two phenomena to establish when connecting fitness and utility is and is not possible.     

Emplotting Hikikomori: Japanese Parents’ Narratives of Social Withdrawal

Hikikomori, often glossed as “social withdrawal,” emerged as a sociomedical condition among Japanese youth at the end of the twentieth century, and it continues to fascinate and concern the public. Explanatory frameworks for hikikomori abound, with different stakeholders attributing it to individual psychopathology, poor parenting, and/or a lack of social support structures. This article takes an interpretive approach to hikikomori by exploring parents’ narrative constructions of hikikomori children in support group meetings and in-depth interviews. I argue that some parents were able to find hope in hikikomori by ‘emplotting’ their children’s experiences into a larger narrative about onset, withdrawal, and recovery, which helped them remain invested in the present by maintaining a sense of possibility about the future. Contrary to literature that examines hikikomori as an epidemic of isolated individuals, I demonstrate how parents play a key role in hikikomori through meaning-making activities that have the potential to shape their children’s experiences of withdrawal.     

Predicting the occurrence of persistent hotspots in ecosystem variables

Ecological resources and services (e.g. organisms, nutrient cycling) are distributed heterogeneously across landscapes. While spatial variation has been studied extensively, the pattern of hotspots and coolspots persisting over time – called persistent spatial variation (PSV) – has not. Yet this pattern imparts key information to managers about whether resources will be found consistently in certain locations or vary unpredictably. Anticipating whether an ecosystem variable will display PSV is thus a valuable prospect. We tested the ability of attributes of variables (e.g. niche breadth, abundance, temporal scale) to predict the occurrence of PSV. Using a new measure of PSV based on the F‐value of analysis of variance, we were able to 1) decompose the pattern of persistent hotspots into spatial and temporal components – ‘spatial variation’ of site mean values and ‘stability’ of time series at each site – and 2) identify predictors of these patterns in temperate lakes and tropical coastal rock pools. We found PSV to be highly predictable (R2 = up to 0.80) from an estimate of stability taken at a single site, as well as from other factors related to stability. These factors included whether the variable was environmental (stable, slow) or was an aggregate of other variables (stabilized by statistical averaging). Species properties like niche position and abundance were modest predictors because they correlated with PSV components of site occupancy, spatial variation and stability. We conclude that PSV and the distribution of resources in space and time might be predicted from simple temporal indicators (e.g. stability at a single location) when data are scarce.     

Natural Selection: A Misnomer Concept

Charles Robert Darwin hypothesized that the mechanism of evolution and the diversity of life on earth are because of natural selection. That is, which biological entity would thrive on earth is a matter of selection by the nature. But, in the present article it is hypothesized that the process of appearance of different types of biological entities and the orientation of these organisms in the space in respect to time are the effects of ‘will force’ of the organisms concerned. That is, the mechanism of evolution is a process of self selection, not natural selection.     

Lateral line deformities in wild and farmed sea bass (Dicentrarchus labrax,L.) and sea bream (Sparus aurata,L.)

The lateral line of aquaculture fishes has rarely been studied although it is a very important anatomical organ that could serve as an inexpensive and easy tool to distinguish farmed from wild individuals. In the present study, lateral line deformities were examined in both wild and farmed sea bass (Dicentrarchus labrax) and sea bream (Sparus aurata) specimens to try to detail all possible differences between them. In order to do so, the morphology of the trunk lateral line in wild and farmed adults was examined whereby two major deformities were observed in both species: the ‘scale pocket’ deformity (14–40% incidence in all groups) where the specialized scales are missing but the canal underneath is present and the scale print is obvious, and the ‘somatic scales’ deformity (14–56% incidence in farmed individuals only) where the missing lateral line is covered with normal somatic scales. Histological examination confirmed the macroscopic observations in that the lateral line mechanism was present – although damaged – beneath the scale pocket deformity and completely absent beneath the somatic scales deformity. It is argued that the scale pocket deformity is a result of an accident during the life of the fish whereas the somatic scales deformity is an actual deformity in development.     

Deficiencies in numerical models of anisotropic nonlinearly elastic materials

Incompressible nonlinearly hyperelastic materials are rarely simulated in finite element numerical experiments as being perfectly incompressible because of the numerical difficulties associated with globally satisfying this constraint. Most commercial finite element packages therefore assume that the material is slightly compressible. It is then further assumed that the corresponding strain-energy function can be decomposed additively into volumetric and deviatoric parts. We show that this decomposition is not physically realistic, especially for anisotropic materials, which are of particular interest for simulating the mechanical response of biological soft tissue. The most striking illustration of the shortcoming is that with this decomposition, an anisotropic cube under hydrostatic tension deforms into another cube instead of a hexahedron with non-parallel faces. Furthermore, commercial numerical codes require the specification of a ‘compressibility parameter’ (or ‘penalty factor’), which arises naturally from the flawed additive decomposition of the strain-energy function. This parameter is often linked to a ‘bulk modulus’, although this notion makes no sense for anisotropic solids; we show that it is essentially an arbitrary parameter and that infinitesimal changes to it result in significant changes in the predicted stress response. This is illustrated with numerical simulations for biaxial tension experiments of arteries, where the magnitude of the stress response is found to change by several orders of magnitude when infinitesimal changes in ‘Poisson’s ratio’ close to the perfect incompressibility limit of 1/2 are made.     

Escape from the Red Queen: an overlooked scenario in coevolutionary studies

Almost all eukaryotic organisms undergo sexual recombination at some stage of their life history. However, strictly asexual organisms should have higher per capita rate of reproduction compared with those that have sex, so the latter must convey some advantage which overrides the reproductive benefit of asexuality. For example, sexual reproduction and recombination may play an important role in allowing organisms to evolutionarily ‘keep up’ with parasites. Host–parasite coevolution can operate via negative frequency‐dependent selection whereby parasite genotypes adapt to infect host genotypes as they become locally common. By producing more genetically diverse offspring with unique genotypes, sexual organisms have an advantage over asexual counterparts. Essentially, sexual hosts are more difficult for coevolving parasites to ‘track’ over time. This scenario has been named the “Red Queen hypothesis”. It refers to a passage in Lewis Carroll's ‘Through the Looking Glass’ in which the Red Queen tells Alice: ‘it takes all the running you can do, to keep in the same place’; this statement resembles the negative frequency‐dependent dynamics of host–parasite coevolution.     

Towards a multi‐trophic extension of metacommunity ecology

Metacommunity theory provides an understanding of how spatial processes determine the structure and function of communities at local and regional scales. Although metacommunity theory has considered trophic dynamics in the past, it has been performed idiosyncratically with a wide selection of possible dynamics. Trophic metacommunity theory needs a synthesis of a few influential axis to simplify future predictions and tests. We propose an extension of metacommunity ecology that addresses these shortcomings by incorporating variability among trophic levels in ‘spatial use properties’. We define ‘spatial use properties’ as a set of traits (dispersal, migration, foraging and spatial information processing) that set the spatial and temporal scales of organismal movement, and thus scales of interspecific interactions. Progress towards a synthetic predictive framework can be made by (1) documenting patterns of spatial use properties in natural food webs and (2) using theory and experiments to test how trophic structure in spatial use properties affects metacommunity dynamics.