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.     

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.     

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.     

Natural distribution

Log-normal distributions describe data from diverse disciplines of science. However, the fundamental basis of log-normal distributions is unknown. We suggest that the skewed distributions are outcomes of natural processes i.e. they result from the principle of increasing entropy. Fluctuations during the course of evolution toward more probable states yield multiplicative variations about the mean. The non-linear dispersion of thermodynamic states, i.e. matter and energy defined by chemical potentials, underlies the skew. Cumulative curves of skewed distributions without integrable analytical forms are characteristic of natural processes.     

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.     

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.     

Revised assignments for the beta-, gamma- and delta-subunits of the acetylcholine receptor structural model

Revised assignments for the bilayer helices of the beta-, gamma- and delta-subunits of the acetylcholine receptor are presented. A new feature of the model is extensive charge matching between the polar groups of the ion channel elements of different subunits.     

Artificial Selection and Domestication: Modern Lessons from Darwin’s Enduring Analogy

It is clear from his published works that Charles Darwin considered domestication to be very useful in exploring and explaining mechanisms of evolutionary change. Not only did domestication occupy the introductory chapter of On the Origin of Species, but he revisited the topic in a two-volume treatise less than a decade later. In addition to drawing much of his information about heredity from studies of domesticated animals and plants, Darwin saw important parallels between the process of artificial selection by humans and natural selection by the environment. There was resistance to this analogy even among Darwin’s contemporary supporters when it was proposed, and there also has been disagreement among historians and philosophers regarding the role that the analogy with artificial selection actually played in the discovery of natural selection. Regardless of these issues, the analogy between artificial and natural selection remains important in both research and education in evolution. In particular, the present article reviews ten lessons about evolution that can be drawn from the modern understanding of domestication and artificial selection. In the process, a basic overview is provided of current approaches and knowledge in this rapidly advancing field.

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.     

Molecular characterization of major histocompatibility complex class II alleles in wild tiger salamanders (Ambystoma tigrinum)

Major histocompatibility complex (MHC) class II genes are usually among the most polymorphic in vertebrate genomes because of their critical role (antigen presentation) in immune response. Prior to this study, the MHC was poorly characterized in tiger salamanders (Ambystoma tigrinum), but the congeneric axolotl (Ambystoma mexicanum) is thought to have an unusual MHC. Most notably, axolotl class II genes lack allelic variation and possess a splice variant without a full peptide binding region (PBR). The axolotl is considered immunodeficient, but it is unclear how or to what extent MHC genetics and immunodeficiency are interrelated. To study the evolution of MHC genes in urodele amphibians, we describe for the first time an expressed polymorphic class II gene in wild tiger salamanders. We sequenced the PBR of a class II gene from wild A. tigrinum (n=33) and identified nine distinct alleles. Observed heterozygosity was 73%, and there were a total of 46 polymorphic sites, most of which correspond to amino acid positions that bind peptides. Patterns of nucleotide substitutions exhibit the signature of diversifying selection, but no recombination was detected. Not surprisingly, transspecies evolution of tiger salamander and axolotl class II alleles was apparent. We have no direct data on the immunodeficiency of tiger salamanders, but the levels of polymorphism in our study population should suffice to bind a variety of foreign peptides (unlike axolotls). Our tiger salamander data suggest that the monomorphism and immunodeficiencies associated with axolotl class II genes is a relict of their unique historical demography, not their phylogenetic legacy. Electronic supplementary material Electronic supplementary material is available for this article at and accessible for authorised users.     

Evolution in Lego ®: A Physical Simulation of Adaptation by Natural Selection

We describe a physical simulation of natural selection in a population of legorgs, six-segment model organisms. Legorg morphology is genetically specified by five alleles on each segment. Legorgs show a simple form of motility that could evolve in originally sessile animals. This motility, the ability to move horizontally on a smooth surface, depends on the morphology and interaction of the six segments that produce different patterns of locomotion. Legorgs are selected for motility and reproduce in proportion to fitness. After just five generations, the average population motility increases 2.5 times. Additionally, we describe a slightly less time-consuming simulation of legorg evolution, where fitness is assigned by comparison with a template. The calculation of gene pools is precisely the same as in the previous simulation and produces very robust increases in fitness during five generations. The simulation is designed as a classroom experiment to explore the mechanism of natural selection. A test of its learning efficiency by evaluating the students’ conception of central aspects of evolutionary theory before and after showed a significant improvement. The surprising power of natural selection in this very simple physical system may also be exploited in more advanced experiments.     

Selection by parasites in spate conditions in wild Trinidadian guppies (Poecilia reticulata)

Gyrodactylids are ubiquitous fish parasites and yet, with the notable exception of Gyrodactylus salaris, few studies have reported the effect of these parasites on host survival in natural populations. Here, we assess the impact of the parasite load of gyrodactylids (G. turnbulli and G. bullatarudis) on the survival and migration of guppies (Poecilia reticulata) in their natural habitat of the Aripo River in Trinidad. The recapture rate of males declined by 19% with every additional parasite, a remarkably high figure given that the parasite load in this study ranged from zero to 20 worms. In addition, with an increased number of parasites, males were more prone to be recovered downstream. In contrast, no effect of parasitism was observed in females. The mean parasite load sharply declined after a series of flushing events during heavy seasonal downpours. The parasite load varied significantly between fish depending on their location in the river, and the size of the fish explained variation in parasite load between individuals. The present study indicates that tropical gyrodactylid parasites can play an important role in the ecology of natural fish populations, causing intense bouts of natural selection in guppies during heavy rains in the wet season.     

Textbooks as a Possible Influence on Unscientific Ideas about Evolution

While school textbooks are assumed to be written for and used by students, it is widely acknowledged that they also serve a vital support function for teachers, particularly in times of curriculum change. A basic assumption is that biology textbooks are scientifically accurate. Furthermore, because of the negative impact of ‘misconceptions’ on learning, it is desirable that textbooks point out common misconceptions and why they are scientifically unacceptable. This paper reports on a study of life sciences textbooks as a potential influence on misconceptions about evolution by natural selection. Textbooks for Grades 10 to 12, from two different publishers, were investigated using content analysis to establish, first, the nature and extent of scientifically incorrect statements about evolution; second, latent problems with wording which might lead to unscientific ideas; and third, whether the books identified and addressed common misconceptions. Unscientific statements were found in all six books, but latent problems associated with the way explanations were expressed were also considered to pose a significant threat to learning. While particularly important for textbook authors and publishers, these findings are also of value to teachers. Although this study was conducted in South Africa, the findings provide useful insights for a wider audience of biology education stakeholders.     

Do Students See the “Selection” in Organic Evolution? A Critical Review of the Causal Structure of Student Explanations

This paper critically reviews and characterizes the student's causal-explanatory understanding; this is done as a step toward explicating the problematic of evolution education as it concerns the cognitive difficulties in understanding Darwin's theory of natural selection. The review concludes that the student's understanding is fundamentally different from Darwin's, for the student understands evolutionary change as necessary individual transformation caused by the transformative action of various physical and behavioral factors. This is in complete contrast to Darwin's (and even the Darwinian's, for that matter) understanding of evolutionary change as a change caused by accumulative selection. Hence, to understand natural selection, the student has to learn to “see” how the accumulative selection causes evolutionary change.

Simulating the maintenance of a rare fish morph experiencing negative frequency dependent selection

Empirical work assessing the maintenance of rare genotypes in natural populations is difficult over very long time scales. Skirting this problematic issue is possible with theory and simulations. Major theoretical constructs, including mutation-selection balance and balancing selection, explain the theoretical maintenance of rare genotypes, and the occurrence of multiple, rare genotypes over time. Additionally, numerical simulations are valuable tools for assessing evolving biological systems because they allow for monitoring systems over long time scales, as well as for controlling model parameters, thus contributing to the exploration of system dynamics that cannot be assessed in nature. Here we employed numerical simulations to explore the importance of several biological factors that contribute to the maintenance of a fish color-pattern polymorphism. We present a numerical model of a two-morph fish polymorphism that allowed us to test the sensitivity of the rare morph's persistence and the population's stability to multiple parameters. Our simulations ran over 10,000 years (where one year is approximately one generation) and demonstrated the maintenance of a stable polymorphism with a rare morph which persisted at a frequency of ∼10⁻², which is in-fact the frequency of the rare, mottled black mosquitofish morph in natural populations. This pigmentation polymorphism is stable, independent of changes in population size, but can be destabilized with very high predation when coupled with very low birth rates. Employing models with empirical fitness estimates is a valuable tool for monitoring rare vertebrate morphs in nature, however few studies exist that have accomplished this task. Our approach can be adapted for modeling rare morphs (particularly in additional live-bearing fishes like sailfin mollies) that also harbor rare, pigmentation morphs within large populations.     

The major androgen-dependent protease in dog prostate belongs to the kallikrein family: confirmation by partial amino acid sequencing

Free energy transduction in active transport resembles other protein-catalyzed processes, occurring by an ordered sequence of discrete bond-breaking and bond-making steps. The bonds that affect the transported ion directly are chelation bonds, which alter the chemical potential of the bound ion, but not its chemical identity. Available data for the sarcoplasmic reticulum Ca pump (admittedly incomplete) suggest that more than 50% of the free energy transfer may be localized to a single step of the reaction cycle.     

不同水分条件下春小麦种群中个体大小不整齐性及遗传学分析不同水分条件下春小麦种群中个体大小不整齐性及遗传学分析

 种群内个体大小不整齐性是种群数量结构的主要指标。本文研究了不同水分条件下,3个品种春小麦种群个体大小不整齐性的建立及变化规律。对春小麦种群不整齐性的遗传学分析表明：遗传结构与随机环境修饰对种群数量结构形成的相对重要性,因水分条件不同而异。种群不整齐性在自然选择中的作用可用下列简单模型表示：CSo＝SH×hSH2 CSo：自然选择强度;SH：大小不整齐性;hSH2：不整齐性的遗传力。     

Maynard Smith,optimization, and evolution

Maynard Smith’s defenses of adaptationism and of the value of optimization theory in evolutionary biology are both criticized. His defense does not adequately respond to the criticism of adaptationism by Gould and Lewontin. It is also argued here that natural selection cannot be interpreted as an optimization process if the objective function to be optimized is either (i) interpretable as a fitness, or (ii) correlated with the mean population fitness. This result holds even if fitnesses are frequency-independent; the problem is further exacerbated in the frequency-dependent context modeled by evolutionary game theory. However, Eshel and Feldman’s new results on “long-term” evolution may provide some hope for the continuing relevance of the game-theoretic framework. These arguments also demonstrate the irrelevance of attempts by Intelligent Design creationists to use computational limits on optimization algorithms as evidence against evolutionary theory. It is pointed out that adaptation, natural selection, and optimization are not equivalent processes in the context of biological evolution. It is a pleasure to dedicate this paper to the memory of John Maynard Smith. Thanks are due to James Justus and Samir Okasha for comments on an earlier draft.     

半干旱区春小麦不同年代品种根系生长冗余的比较实验研究

 研究了半干旱区几个春小麦品种的籽实产量、根量与根茎比的关系。表明在开花期地方品种和尚头较之现代品种有更大的根量和根茎比。产量因降水条件而不同：极端干旱的1995年,大根系品种与现代品种产量无显著差异(p>0.05);在降水分配较为均匀的1996年,无论有、无灌溉条件,具较大根系的地方品种与现代品种的产量均最低(p<0.05),而根量与品种产量及地上生物量呈显著的负相关。表明大根系品种在根系上存在着冗余,减少根系冗余可望成为半干旱区小麦高产育种的一条有效途径。     

Optimality modeling in a suboptimal world

The fate of optimality modeling is typically linked to that of adaptationism: the two are thought to stand or fall together (Gould and Lewontin, Proc Relig Soc Lond 205:581–598, 1979; Orzack and Sober, Am Nat 143(3):361–380, 1994). I argue here that this is mistaken. The debate over adaptationism has tended to focus on one particular use of optimality models, which I refer to here as their strong use. The strong use of an optimality model involves the claim that selection is the only important influence on the evolutionary outcome in question and is thus linked to adaptationism. However, biologists seldom intend this strong use of optimality models. One common alternative that I term the weak use simply involves the claim that an optimality model accurately represents the role of selection in bringing about the outcome. This and other weaker uses of optimality models insulate the optimality approach from criticisms of adaptationism, and they account for the prominence of optimality modeling (broadly construed) in population biology. The centrality of these uses of optimality models ensures a continuing role for the optimality approach, regardless of the fate of adaptationism.