Are individuals really subordinated to genes? A theory of living entities

Modern evolutionary theory consists of an explicit theory of change and an implicit theory of the existence of living entities. A theory of the latter type, called the theory of the process of living (POL), is proposed. It contains a two-level definition of living entities, an analysis of possible and impossible similarity and differences between parents and offspring, and a logical division of the information governing the functioning of a living organism. The theory of POL emphasizes the proceeding of living entities in time while the modern evolutionary theory emphasizes the types of entities proceeding in time. The theory of POL produces a basis for reanalysing relations between individuals, their genes and the environment. It produces some predictions deviating from classic evolutionary theory. These conflicts occur in areas where analyses of genetic dynamics have made implicit assumptions of rules of POL. For example, the theory of POL states that the genetic relatedness of successive generations is a technical solution more than the reason of reproduction, that genetic relatedness as such does not imply altruism between individuals and that genes are the tools whereby organisms exist and not the contrary. Implications of the theory of POL on paradoxes of evolutionary theory are discussed.     

The merits of neutral theory

Hubbell's neutral theory of biodiversity has challenged the classic niche-based view of ecological community structure. Although there have been many attempts to falsify Hubbell's theory, we argue that falsification should not lead to rejection, because there is more to the theory than neutrality alone. Much of the criticism has focused on the neutrality assumption without full appreciation of other relevant aspects of the theory. Here, we emphasize that neutral theory is also a stochastic theory, a sampling theory and a dispersal-limited theory. These important additional features should be retained in future theoretical developments of community ecology.     

Fuzzy systems vegetation theory

Fuzzy systems vegetation theory is a comprehensive framework for the expression of vegetation theory and conceptual models, as well as the development of vegetation analyses. It is applicable to vegetation/environment relations, vegetation dynamics, and the effects of environmental dynamics on vegetation composition. Fuzzy systems vegetation theory is a fuzzy set generalization of dynamical systems theory and incorporates a formal logic and mathematics. This paper presents the elements of fuzzy systems vegetation theory and discusses the relationship of the fuzzy systems theory to the geometric concepts generally employed in vegetation theory.     

Neutral theory in community ecology

One of the central goals of community ecology is to understand the forces that maintain species diversity within communities. The traditional niche-assembly theory asserts that species live together in a community only when they differ from one another in resource uses. But this theory has some difficulties in explaining the diversity often observed in specie-rich communities such as tropical forests. As an alternative to the niche theory, Hubbell and other ecologists introduced a neutral model. Hubbell argues that the number of species in a community is controlled by species extinction and immigration or speciation of new species. Assuming that all individuals of all species in a trophically similar com-munity are ecologically equivalent, Hubbell's neutral theory predicts two important statistical distributions. One is the asymptotic log-series distribution for the metacommunities under point mutation speciation, and the other is the zero-sum multinomial distribution for both local communities under dispersal limitation and metacommunities under random fission speciation. Unlike the niche-assembly theory, the neutral theory takes similarity in species and individuals as a starting point for investigating species diversity. Based on the fundamental processes of birth, death, dispersal and spe-ciation, the neutral theory provided the first mechanistic explanation of species abundance distribution commonly observed in natural communities. Since the publication of the neutral theory, there has been much discussion about it, pro and con. In this paper, we summarize recent progress in the assumption, prediction and speciation mode of the neutral theory, including progress in the theory itself, tests about the assumption of the theory, prediction and speciation mode at the metacommunity level. We also suggest that the most important task in the future is to bridge the niche-assembly theory and the neutral theory, and to add species differences to the neutral theory and more stochasticity to the niche theory.     

群落生态学的中性理论

生物多样性的分布格局和维持机制一直是群落生态学研究的核心问题,其中的关键是物种的共存机制。长期以来,生态位分化的思想在这一研究领域占据着主导地位。然而这一理论在解释热带雨林很高的物种多样性时遇到了困难。而以Hubbell为代表提出的群落中性漂变理论则假定在同一营养级物种构成的群落中不同物种的不同个体在生态学上可看成是完全等同的;物种的多度随机游走,群落中的物种数取决于物种灭绝和物种迁入/新物种形成之间的动态平衡。在这一假定之下,该理论预言了两种统计分布。一种是集合群落在点突变形成新物种的模式下其各个物种相对多度服从对数级数分布,而受扩散限制的局域群落以及按照随机分裂为新物种模式形成的集合群落则服从零和多项式分布。与生态位理论相反,中性理论不以种间生态位差异作为研究群落结构的出发点,而是以物种间在个体水平上的对等性作为前提。该理论第一次从基本生态学过程(出生、死亡、迁移、物种分化)出发,给出了群落物种多度分布的机理性解释,同时其预测的物种多度分布格局在实际群落中也得到了广泛的印证。因此,中性理论自诞生以来便在生态学界引发了极大的反响,也包括一些反对的声音。该文重点综述了关于中性理论的假设、预测和物种形成模式等方面的最新研究进展,包括中性理论本身的发展、关于中性理论的假设和预测的合理性检验以及在集合群落尺度上物种分化模式的讨论;并指出未来发展方向可能是在生态位理论和中性理论之间架起一座桥梁,同时发展包含随机性的群落生态位模型,以及允许种间差异的近中性模型。     

A Turing test of a timing theory

A quantitative theory of timing or conditioning can be evaluated with a Turing test in which the behavioral results of an experiment can be compared with the predicted results from the theory. An example is described based upon an experiment in which 12 rats were trained on three fixed-interval schedules of reinforcement, and a simulation of the predicted results from a packet theory of timing. An objective classification rule was used to determine whether a sample from the data or a sample from the theory was more similar to another sample from the theory. With an ideal theory, the expected probability of a correct classification would be 0.5. The observed probability of a correct classification was 0.6, which was slightly, but reliably, greater than 0.5. A Turing test provides a graded metric for the evaluation of a quantitative theory.     

The Need for a Kinetics for Biological Transport

The traditional theory of transport across capillary membranes via a laminar Poiseuille flow is shown to be invalid. It is demonstrated that the random, diffusive nature of the molecular flow and interactions with the “pore” walls play an important role in the transport process. Neither the continuum Navier-Stokes theory nor the equivalent theory of irreversible thermodynamics is adequate to treat the problem. Combination of near-continuum hydrodynamic theory, noncontinuum kinetic theory, and the theory of fluctuations provides a first step toward modeling both liquid processes in general and membrane transport processes as a specific application.     

Behavioral and neural Darwinism: Selectionist function and mechanism in adaptive behavior dynamics

An evolutionary theory of behavior dynamics and a theory of neuronal group selection share a common selectionist framework. The theory of behavior dynamics instantiates abstractly the idea that behavior is selected by its consequences. It implements Darwinian principles of selection, reproduction, and mutation to generate adaptive behavior in virtual organisms. The behavior generated by the theory has been shown to be quantitatively indistinguishable from that of live organisms. The theory of neuronal group selection suggests a mechanism whereby the abstract principles of the evolutionary theory may be implemented in the nervous systems of biological organisms. According to this theory, groups of neurons subserving behavior may be selected by synaptic modifications that occur when the consequences of behavior activate value systems in the brain. Together, these theories constitute a framework for a comprehensive account of adaptive behavior that extends from brain function to the behavior of whole organisms in quantitative detail.     

Neutral theory in community ecology

One of the central goals of community ecology is to understand the forces that maintain species diversity within communities. The traditional niche-assembly theory asserts that species live together in a community only when they differ from one another in resource uses. But this theory has some difficulties in explaining the diversity often observed in specie-rich communities such as tropical forests. As an alternative to the niche theory, Hubbell and other ecologists introduced a neutral model. Hubbell argues that the number of species in a community is controlled by species extinction and immigration or speciation of new species. Assuming that all individuals of all species in a trophically similar community are ecologically equivalent, Hubbell’s neutral theory predicts two important statistical distributions. One is the asymptotic log-series distribution for the metacommunities under point mutation speciation, and the other is the zero-sum multinomial distribution for both local communities under dispersal limitation and metacommunities under random fission speciation. Unlike the niche-assembly theory, the neutral theory takes similarity in species and individuals as a starting point for investigating species diversity. Based on the fundamental processes of birth, death, dispersal and speciation, the neutral theory provided the first mechanistic explanation of species abundance distribution commonly observed in natural communities. Since the publication of the neutral theory, there has been much discussion about it, pro and con. In this paper, we summarize recent progress in the assumption, prediction and speciation mode of the neutral theory, including progress in the theory itself, tests about the assumption of the theory, prediction and speciation mode at the metacommunity level. We also suggest that the most important task in the future is to bridge the niche-assembly theory and the neutral theory, and to add species differences to the neutral theory and more stochasticity to the niche theory. __________ Translated from Journal of Plant Ecology, 2006, 30(5): 868–877 [译自:植物生态学报]     

Can the theory of evolution be falsified?

In this paper we discuss the epistemological positions of evolution theories. A sharp distinction is made between the theory that species evolved from common ancestors along specified lines of descent (here called the theory of common descent), and the theories intended as causal explanations of evolution (e.g. Lamarck's and Darwin's theory). The theory of common descent permits a large number of predictions of new results that would be improbable without evolution. For instance, (a) phylogenetic trees have been validated now; (b) the observed order in fossils of new species discovered since Darwin's time could be predicted from the theory of common descent; (c) owing to the theory of common descent, the degrees of similarity and difference in newly discovered properties of more or less related species could be predicted. Such observations can be regarded as attempts to falsify the theory of common descent. We conclude that the theory of common descent is an easily-falsifiable & often-tested & still-not-falsified theory, which is the strongest predicate a theory in an empirical science can obtain. Theories intended as causal explanations of evolution can be falsified essentially, and Lamarck's theory has been falsified actually. Several elements of Darwin's theory have been modified or falsified: new versions of a theory of evolution by natural selection are now the leading scientific theories on evolution. We have argued that the theory of common descent and Darwinism are ordinary, falsifiable scientific theories.     

自然保护区学说与麦克阿瑟-威尔逊理论

全球正两临着一场物种灭绝的大危机,自然保护己成为人类面临的重大课题,自然保护区的建立是减缓物种灭绝速率、保护生物多样性的重要途径。岛屿生物地理学为自然保护区理论的产生起了重要的作用。然而,许多研究表明,该学科尚未成熟,尤其在自然保护区方面的应用颇为有限,无疑,现代自然保护区理论应是多学科研究的综合产物。本文概述了岛屿生物地理学的基本内容及其在自然保护方面的影响,并对种群脆性分析和景观生态学途径在自然保护区理论中的作用进行讨论。     

Deconstructing Darwin: Evolutionary theory in context

The topic of this paper is external versus internal explanations, first, of the genesis of evolutionary theory and, second, its reception. Victorian England was highly competitive and individualistic. So was the view of society promulgated by Malthus and the theory of evolution set out by Charles Darwin and A.R. Wallace. The fact that Darwin and Wallace independently produced a theory of evolution that was just as competitive and individualistic as the society in which they lived is taken as evidence for the impact that society has on science. The same conclusion is reached with respect to the reception of evolutionary theory. Because Darwins contemporaries lived in such a competitive and individualistic society, they were prone to accept a theory that exhibited these same characteristics. The trouble is that Darwin and Wallace did not live in anything like the same society and did not formulate the same theory. Although the character of Victorian society may have influenced the acceptance of evolutionary theory, it was not the competitive, individualistic theory that Darwin and Wallace set out but a warmer, more comforting theory.     

An assessment of Gallistel's (2012) rationalistic account of extinction phenomena

Gallistel (2012) asserts that animals use rationalistic reasoning (i.e., information theory and Bayesian inference) to make decisions that underlie select extinction phenomena. Rational processes are presumed to lead to evolutionarily optimal behavior. Thus, Gallistel's model is a type of optimality theory. But optimality theory is only a theory, a theory about an ideal organism, and its predictions frequently deviate appreciably from observed behavior of animals in the laboratory and the real world. That is, behavior of animals is often far from optimal, as is evident in many behavioral phenomena. Hence, appeals to optimality theory to explain, rather than illuminate, actual behavior are misguided.     

The validity and value of inclusive fitness theory

Social evolution is a central topic in evolutionary biology, with the evolution of eusociality (societies with altruistic, non-reproductive helpers) representing a long-standing evolutionary conundrum. Recent critiques have questioned the validity of the leading theory for explaining social evolution and eusociality, namely inclusive fitness (kin selection) theory. I review recent and past literature to argue that these critiques do not succeed. Inclusive fitness theory has added fundamental insights to natural selection theory. These are the realization that selection on a gene for social behaviour depends on its effects on co-bearers, the explanation of social behaviours as unalike as altruism and selfishness using the same underlying parameters, and the explanation of within-group conflict in terms of non-coinciding inclusive fitness optima. A proposed alternative theory for eusocial evolution assumes mistakenly that workers' interests are subordinate to the queen's, contains no new elements and fails to make novel predictions. The haplodiploidy hypothesis has yet to be rigorously tested and positive relatedness within diploid eusocial societies supports inclusive fitness theory. The theory has made unique, falsifiable predictions that have been confirmed, and its evidence base is extensive and robust. Hence, inclusive fitness theory deserves to keep its position as the leading theory for social evolution.     

Minimal reduplication and reduplicative exponence

This paper presents Minimal Reduplication, a theory which analyzes reduplication as an emergent phenomenon. The theory is discussed with special focus on the area of morphophonology. Key claims and architecture are discussed in some detail. Finally a case study of a complex set of reduplicative data is considered in order to illustrate the utility of the theory and how the theory is deployed.     

How do birds' tails work? Delta-wing theory fails to predict tail shape during flight.

Birds appear to use their tails during flight, but until recently the aerodynamic role that tails fulfil was largely unknown. In recent years delta-wing theory, devised to predict the aerodynamics of high-performance aircraft, has been applied to the tails of birds and has been successful in providing a model for the aerodynamics of a bird's tail. This theory now provides the conventional explanation for how birds' tails work. A delta-wing theory (slender-wing theory) has been used, as part of a variable-geometry model to predict how tail and wing shape should vary during flight at different airspeeds. We tested these predictions using barn swallows flying in a wind tunnel. We show that the predictions are not quantitatively well supported. This suggests that a new theory or a modified version of delta-wing theory is needed to adequately explain the way in which morphology varies during flight.     

On mutant sets

This paper sketches the outline of a new, general mathematical theory concerning the nature of a relative anti-closure property for subsets of general algebraic systems. It thus quite naturally fits into any exhaustive theory of relations and, in particular, into a theory of relations for abstract mathematical molecular biology. In addition, the theory possesses certain intuitive, but naive relationships to basic analytical studies of biological mating and mutation. At the purely mathematical level one can produce an abundance of theorems from the theory with interpretations in the context of the frequently appearing mathematical structures of groups and rings, among other algebraic structures.     

A test of the humped-back theory of species richness in New Zealand native forest

The Humped-back theory of plant species richness, a theory related to Grime's C-S-R 'triangular' model, has been widely discussed, and some evidence has been claimed in support of it. The theory suggests that species richness is maximal at intermediate levels of productivity, i.e., at intermediate positions on a stress/favourability gradient. We sought evidence for the theory from 90 stands of native podocarp/broadleaved and beech forest in the Coastal Otago region, with an adjustment made for the effect of stand area on species richness. There was no relation between adjusted species richness and an index of site stress/favourability, i.e., no support for the Humped-back theory. The theory may be inapplicable to woody vegetation, or it may be applicable only when the 'favourable' end of the spectrum comprises agricultural communities, or support for the theory might be inflated in the literature by a wish to find ecological generalisations.     

The reliability theory of aging and longevity.

Reliability theory is a general theory about systems failure. It allows researchers to predict the age-related failure kinetics for a system of given architecture (reliability structure) and given reliability of its components. Reliability theory predicts that even those systems that are entirely composed of non-aging elements (with a constant failure rate) will nevertheless deteriorate (fail more often) with age, if these systems are redundant in irreplaceable elements. Aging, therefore, is a direct consequence of systems redundancy. Reliability theory also predicts the late-life mortality deceleration with subsequent leveling-off, as well as the late-life mortality plateaus, as an inevitable consequence of redundancy exhaustion at extreme old ages. The theory explains why mortality rates increase exponentially with age (the Gompertz law) in many species, by taking into account the initial flaws (defects) in newly formed systems. It also explains why organisms "prefer" to die according to the Gompertz law, while technical devices usually fail according to the Weibull (power) law. Theoretical conditions are specified when organisms die according to the Weibull law: organisms should be relatively free of initial flaws and defects. The theory makes it possible to find a general failure law applicable to all adult and extreme old ages, where the Gompertz and the Weibull laws are just special cases of this more general failure law. The theory explains why relative differences in mortality rates of compared populations (within a given species) vanish with age, and mortality convergence is observed due to the exhaustion of initial differences in redundancy levels. Overall, reliability theory has an amazing predictive and explanatory power with a few, very general and realistic assumptions. Therefore, reliability theory seems to be a promising approach for developing a comprehensive theory of aging and longevity integrating mathematical methods with specific biological knowledge.