Natural hierarchy emerges from energy dispersal

Hierarchical organization of ‘systems within systems’ is an apparent characteristic of nature. For many biotic and abiotic systems it is known how the nested structural and functional order builds up, yet the general principle why matter evolves to hierarchies has remained unfamiliar to many. We clarify that increasingly larger integrated systems result from the quest to decrease free energy according to the 2nd law of thermodynamics. The argumentation is based on the recently derived equation of motion for natural processes. Hierarchically organized energy transduction machinery emerges naturally when it provides increased rates of energy dispersal. Likewise, a hierarchical system will dismantle into its constituents when they as independent systems will provide higher rates of entropy increase. Since energy flows via interactions, decreasing strengths of interactions over increasingly larges lengths scales mark natural boundaries for nested integrated systems.     

Ecological succession as an energy dispersal process

Ecological succession is described by the 2nd law of thermodynamics. According to the universal law of the maximal energy dispersal, an ecosystem evolves toward a stationary state in its surroundings by consuming free energy via diverse mechanisms. Species are the mechanisms that conduct energy down along gradients between repositories of energy which consist of populations at various thermodynamic levels. The salient characteristics of succession, growing biomass production, increasing species richness and shifting distributions of species are found as consequences of the universal quest to diminish energy density differences in least time. The analysis reveals that during succession the ecosystem's energy transduction network, i.e., the food web organizes increasingly more effective in the free energy reduction by acquiring new, more effective and abandoning old, less effective species of energy transduction. The number of species does not necessarily peak at the climax state that corresponds to the maximum-entropy partition of species maximizing consumption of free energy. According to the theory of evolution by natural selection founded on statistical physics of open systems, ecological succession is one among many other evolutionary processes.     

Gaia again

The ideas of the Gaia hypothesis from the 1960s are today largely included in global ecology and Earth system sciences. The interdependence between biosphere, oceans, atmosphere and geosphere is well-established by data from global monitoring. Nevertheless the theory underlying the holistic view of the homeostatic Earth has remained obscure. Here the foundations of Gaia theory are examined from the recent formulation of the 2nd law of thermodynamics as an equation of motion. According to the principle of increasing entropy, all natural processes, inanimate just as animate, consume free energy, the thermodynamic driving force. All species, abiotic just as biotic are viewed as mechanisms of energy transduction for the global system to evolve toward a stationary state in its surroundings. The maximum entropy state displays homeostasis by being stable against internal fluctuations. When surrounding conditions change or when new mechanisms emerge, the global system readjusts its flows of energy to level newly appeared gradients. Thus, the propositions of Gaia theory and holistic understanding of the global system are recognized as consequences of thermodynamic imperatives.     

Are organisms committed to lower their rates of entropy production?: Possible relevance to evolution of the Prigogine theorem and the ergodic hypothesis

The physiology at limiting and stress conditions challenges the current view that the overall reaction of metabolic processes is always far from equilibrium and, therefore, that organisms are not committed to lower their rates of entropy production. Plausibly, critical steps of natural selection takes place at limiting conditions, near equilibrium, in the linear range response of entropy production, and consequently the trend to lower the rate of entropy production could be the fitness arrow of biological evolution. The evolutionary relevance of the Prigogine theorem is discussed in connection with the ergodic hypothesis of Boltzmann. The emergence of metabolic strategies to economise carbon/energy resources, of resource-waste systems like active transport and the irreversible increase in the complexity of organisms during evolution may be consequences of a more general trend of metabolic systems to lower the rates of entropy production.     

Addressing Undergraduate Student Misconceptions about Natural Selection with an Interactive Simulated Laboratory

Although evolutionary theory is considered to be a unifying foundation for biological education, misconceptions about basic evolutionary processes such as natural selection inhibit student understanding. Even after instruction, students harbor misconceptions about natural selection, suggesting that traditional teaching methods are insufficient for correcting these confusions. This has spurred an effort to develop new teaching methods and tools that effectively confront student misconceptions. In this study, we designed an interactive computer-based simulated laboratory to teach the principles of evolution through natural selection and to correct common student misconceptions about this process. We quantified undergraduate student misconceptions and understanding of natural selection before and after instruction with multiple-choice and open-response test questions and compared student performance across gender and academic levels. While our lab appeared to be effective at dispelling some common misconceptions about natural selection, we did not find evidence that it was as successful at increasing student mastery of the major principles of natural selection. Student performance varied across student academic level and question type, but students performed equally across gender. Beginner students were more likely to use misconceptions before instruction. Advanced students showed greater improvement than beginners on multiple-choice questions, while beginner students reduced their use of misconceptions in the open-response questions to a greater extent. These results suggest that misconceptions can be effectively addressed through computer-based simulated laboratories. Given the level of misconception use by beginner and advanced undergraduates and the gains in performance recorded after instruction at both academic levels, natural selection should continue to be reviewed through upper-level biology courses.     

Novel bivariate moment-closure approximations

Nonlinear stochastic models are typically intractable to analytic solutions and hence, moment-closure schemes are used to provide approximations to these models. Existing closure approximations are often unable to describe transient aspects caused by extinction behaviour in a stochastic process. Recent work has tackled this problem in the univariate case. In this study, we address this problem by introducing novel bivariate moment-closure methods based on mixture distributions. Novel closure approximations are developed, based on the beta-binomial, zero-modified distributions and the log-Normal, designed to capture the behaviour of the stochastic SIS model with varying population size, around the threshold between persistence and extinction of disease. The idea of conditional dependence between variables of interest underlies these mixture approximations. In the first approximation, we assume that the distribution of infectives (I) conditional on population size (N) is governed by the beta-binomial and for the second form, we assume that I is governed by zero-modified beta-binomial distribution where in either case N follows a log-Normal distribution. We analyse the impact of coupling and inter-dependency between population variables on the behaviour of the approximations developed. Thus, the approximations are applied in two situations in the case of the SIS model where: (1) the death rate is independent of disease status; and (2) the death rate is disease-dependent. Comparison with simulation shows that these mixture approximations are able to predict disease extinction behaviour and describe transient aspects of the process.     

Suitable microscopic entropy for the origin of microbial life: Microbiological methods are challenges

A hypothesis is proposed that the first living microbial cell(s) on Earth assembled about 3.6-4 billion years ago when an environmental microscopic entropy (balance between order and disorder; suitable amount of randomness) was within a range suitable for the origin of microbial cell(s) in a hydrogel environment. An earlier origin of microbial life was not possible as the elements, molecules and entropy conditions necessary for life were not available at the microscopic level. Methodology limitations to study postulated past origin of microbial life events and to mimic these events in the laboratory, are still obstacles to understanding the origin of life.     

Animals in science education—ethics and alternatives

Increasingly, moral objections are being voiced to the use or killing of animals for educational purposes, and students' opinions are reflecting this. An animal rights philosophy often underlies these objections, but many people are unaware of the logic of the animal rights position, which is often dismissed as sentimentalism or anthropomorphism. While it is now possible to take A-level biology without undertaking dissection, there are many potential undergraduate students who would like to do courses in biology, medicine, pharmacology, physiology, and nursing, but are dissuaded by the animal use involved. Such students are frequently not offered non-animal options and risk being marked down in course work and exams, even though considerable advances have been made in the development of alternative teaching aids. This article summarizes the animal rights argument, and reviews some of the alternative approaches and their teaching effectiveness.     

The ideal free distribution as an evolutionarily stable strategy

We examine the evolutionary stability of strategies for dispersal in heterogeneous patchy environments or for switching between discrete states (e.g. defended and undefended) in the context of models for population dynamics or species interactions in either continuous or discrete time. There have been a number of theoretical studies that support the view that in spatially heterogeneous but temporally constant environments there will be selection against unconditional, i.e. random, dispersal, but there may be selection for certain types of dispersal that are conditional in the sense that dispersal rates depend on environmental factors. A particular type of dispersal strategy that has been shown to be evolutionarily stable in some settings is balanced dispersal, in which the equilibrium densities of organisms on each patch are the same whether there is dispersal or not. Balanced dispersal leads to a population distribution that is ideal free in the sense that at equilibrium all individuals have the same fitness and there is no net movement of individuals between patches or states. We find that under rather general assumptions about the underlying population dynamics or species interactions, only such ideal free strategies can be evolutionarily stable. Under somewhat more restrictive assumptions (but still in considerable generality), we show that ideal free strategies are indeed evolutionarily stable. Our main mathematical approach is invasibility analysis using methods from the theory of ordinary differential equations and nonnegative matrices. Our analysis unifies and extends previous results on the evolutionary stability of dispersal or state-switching strategies.     

Some genetic consequences of skewed fecundity distributions in plants

Summary Most plant populations show a skewedrd distribution of fecundity amongst their members, in contrast to the poisson distribution assumed by most population genetical theory. We examine by simulation the consequences of skewed fecundity for plant evolution when combined with sieve selection. In comparison with poisson-based theory, plant populations are likely to show a faster response to selection, especially when the favoured allele is at a low frequency. Selection against a deleterious immigrant allele will also be more effective, reducing its equilibrium frequency in a population. In the special case of heterozygote disadvantage traits will evolve that could not under poisson theory. However, random variation is also higher, giving a 10-plant population an effective population size of about 6.4 under poisson theory. The conclusions are not qualitatively changed by different assumptions on the exact shape of the fecundity distribution, or on heritability, or on reproduction by the smallest plants of the population.     

Geographical distribution and phenotypic differentiation in populations of Dactylis glomerata L. in Japan

Although the perennial grass Dactylis glomerata L. has established dominant populations in Japan since its introduction in the 1870s, there have been marked reductions in its abundance in southern and northeastern regions. In order to examine the effects of climatic factors on distribution and differentiation of the naturalized populations of D. glomerata, abundance of 26 populations over a distance of 1500 km along a latitudinal gradient was recorded at each site, and life-history traits of each population were measured in a common garden. It was found that the reduction in abundance was related to the mean summer temperature in southern regions and to the lowest temperature before snow cover in northeastern regions. Recent climatic records in Japan show an increase in the mean summer temperature but no apparent changes in the lowest temperature before snow cover. These data suggest that, assuming the recent trend in climatic changes continues, the population abundance will decrease in southern regions and will change little in the northeastern regions. Germination speed, leaf width and reproductive allocations showed clinal variation over a geographical range, and the southern populations had more rapid germination, narrower leaves and lower reproductive allocation than did the northern populations. On the other hand, seed size and germination date showed margin-center differentiation. Marginal populations in both distributional borders had smaller seeds and lower germination rates than did the central populations. This revised version was published online in June 2006 with corrections to the Cover Date.     

Seed dispersal curves: Behavior of the tail of the distribution

Summary Seed dispersal is important both to plant fitness and to plant population structure. We suggest that the tail of the seed dispersal curve is at least as important biologically as the modal portion of the curve, and we present a relatively simple, four-parameter model, based on diffusion principles, for the tail of the seed distribution. This model includes two types of qualitative behavior: algebraic tails (which tend to be longer and have greater reach) and exponential tails (which are shorter and have less reach). We have selected 68 data sets from the literature, each giving a seed shadow that could be categorized statistically as (1) exponential, (2) algebraic, (3) neither, or (4) both models fit adequately. Algebraic shapes for seed-shadow tails were common in this sample, and tail behavior was not generally specific to a particular dispersal mode. This result may suggest that algebraic tails are generally favored by selection and can be achieved by several means, but limitations of existing data sets and of statistical methodology preclude final judgement. Smaller complete samples of seed distances would provide a better basis for the analysis of tails than do the present form of data sets (consisting of counts of seeds in discrete distance categories).     

Size structure and dynamics of some woody perennials along elevation gradient in Wadi Gimal, Red Sea coast of Egypt

The population structure of 10 common woody perennials was investigated in terms of size distribution, height, diameter and density in Wadi Gimal along the Red Sea coast of Egypt. It was attempted to assess the effect of elevation on the size, distribution and density of the studied species. These species are: five trees (Acacia tortilis subsp. raddiana, Acacia tortilis subsp. tortilis, Balanites aegyptiaca, Tamarix aphylla, and Tamarix nilotica), two shrubs (Leptadenia pyrotechnica and Nitraria retusa) and three shrublets (Pulicaria undulata, Zilla spinosa, and Zygophyllum coccineum). The size estimations were then used to classify population into six size classes: 20-80 cm for shrublets, 100-500 cm for shrubs, and 2-10 m for trees. The absolute and relative frequency of individuals and mean height, diameter and height to diameter ratio per individual in each size class were determined. Density of occurrence of most species, except B. aegyptiaca, decreased as elevation increased. The height-to-diameter ratio was less than unity for most of the recorded species except T. nilotica. Several forms - including, positively and negatively skewed, inverse J-shaped, bell shaped and more or less J-shaped distributions - were recognized along the different elevations. The size structure of some species was positively related with soil variables, such as T. nilotica with sulphate, while some others were negatively significant related to the substrate characteristics, such as Z. spinosa with salinity.     

Natural selection and veridical perceptions

Does natural selection favor veridical perceptions, those that more accurately depict the objective environment? Students of perception often claim that it does. But this claim, though influential, has not been adequately tested. Here we formalize the claim and a few alternatives. To test them, we introduce “interface games,” a class of evolutionary games in which perceptual strategies compete. We explore, in closed-form solutions and Monte Carlo simulations, some simpler games that assume frequency-dependent selection and complete mixing in infinite populations. We find that veridical perceptions can be driven to extinction by non-veridical strategies that are tuned to utility rather than objective reality. This suggests that natural selection need not favor veridical perceptions, and that the effects of selection on sensory perception deserve further study.     

The significance of sex

Sexual and asexual modes of proliferation are associated with advantages and disadvantages, yet a profound percept that would account for both ways of reproduction is missing. On the basis of the 2nd law of thermodynamics we find that both sexual and asexual reproduction can be regarded as a means to consume free energy in least time. Parthenogenesis is a fast way to consume a rich repository of free energy, e.g., an ample stock of food with a large number of individuals, whereas sexual reproduction is a fast way to consume diverse and dispersed resources with a large variety of individuals. Most organisms have adapted to their surroundings accordingly and some organisms switch from one mode of reproduction to the other depending on the amount and dispersion of free-energy sources. We conclude that the least-time free energy consumption in respective surroundings, as the general criterion of natural selection, determines also sexual and asexual modes of reproduction.