生殖叶学说与心皮学说

本文介绍了Melvill提出的生殖叶学说中的有关生殖叶的概念,雌蕊和雄蕊的起源及同种演化方式。并结合心皮学说进行了讨论。     

Biology Needs Information Theory

Communication is an important feature of the living world that mainstream biology fails to adequately deal with. Applying two main disciplines can be contemplated to fill in this gap: semiotics and information theory. Semiotics is a philosophical discipline mainly concerned with meaning; applying it to life already originated in biosemiotics. Information theory is a mathematical discipline coming from engineering which has literal communication as purpose. Biosemiotics and information theory are thus concerned with distinct and complementary possible meanings of the word ‘communication’. Since literal communication needs to be secured so as to enable semantics being communicated, information theory is a necessary prerequisite to biosemiotics. Moreover, heredity is a purely literal communication process of capital importance fully relevant to literal communication, hence to information theory. A short introduction to discrete information theory is proposed, which is centred on the concept of redundancy and its use in order to make sequences resilient to errors. Information theory has been an extremely active and fruitful domain of researches and the motor of the tremendous progress of communication engineering in the last decades. Its possible connections with semantics and linguistics are briefly considered. Its applications to biology are suggested especially as regards error-correcting codes which are mandatory for securing the conservation of genomes. Biology needs information theory so biologists and communication engineers should closely collaborate.     

Multiple Explanations in Darwinian Evolutionary Theory

Variational evolutionary theory as advocated by Darwin is not a single theory, but a bundle of related but independent theories, namely: (a) variational evolution; (b) gradualism rather than large leaps; (c) processes of phyletic evolution and of speciation; (d) causes for the formation of varying individuals in populations and for the action of selective agents; and (e) all organisms evolved from a common ancestor. The first four are nomological-deductive explanations and the fifth is historical-narrative. Therefore evolutionary theory must be divided into nomological and historical theories which are both testable against objective empirical observations. To be scientific, historical evolutionary theories must be based on well corroborated nomological theories, both evolutionary and functional. Nomological and general historical evolutionary theories are well tested and must be considered as strongly corroborated scientific theories. Opponents of evolutionary theory are concerned only with historical evolutionary theories, having little interest in nomological theory. Yet given a well corroborated nomological evolutionary theory, historical evolutionary theories follow automatically. If understood correctly, both forms of evolutionary theories stand on their own as corroborated scientific theories and should not be labeled as facts.     

Theory and speciation

The study of speciation has become one of the most active areas of evolutionary biology, and substantial progress has been made in documenting and understanding phenomena ranging from sympatric speciation and reinforcement to the evolutionary genetics of postzygotic isolation. This progress has been driven largely by empirical results, and most useful theoretical work has concentrated on making sense of empirical patterns. Given the complexity of speciation, mathematical theory is subordinate to verbal theory and generalizations about data. Nevertheless, mathematical theory can provide a useful classification of verbal theories; can help determine the biological plausibility of verbal theories; can determine whether alternative mechanisms of speciation are consistent with empirical patterns; and can occasionally provide predictions that go beyond empirical generalizations. We discuss recent examples of progress in each of these areas.     

Theory and practice of ultra-perfection

Perfection has been used as a criteria to classify rearrangement scenarios since 2004. However, there is a fundamental bias towards extant species in the original definition: ancestral species are not bound to perfection. Here we develop a new theory of perfection that takes an egalitarian view of species, and we examine the fitness of this theory on several datasets. Supplementary Material is available at www.liebertonline.com/cmb.     

Game Theory of Mind

This paper introduces a model of ‘theory of mind’, namely, how we represent the intentions and goals of others to optimise our mutual interactions. We draw on ideas from optimum control and game theory to provide a ‘game theory of mind’. First, we consider the representations of goals in terms of value functions that are prescribed by utility or rewards. Critically, the joint value functions and ensuing behaviour are optimised recursively, under the assumption that I represent your value function, your representation of mine, your representation of my representation of yours, and so on ad infinitum. However, if we assume that the degree of recursion is bounded, then players need to estimate the opponent's degree of recursion (i.e., sophistication) to respond optimally. This induces a problem of inferring the opponent's sophistication, given behavioural exchanges. We show it is possible to deduce whether players make inferences about each other and quantify their sophistication on the basis of choices in sequential games. This rests on comparing generative models of choices with, and without, inference. Model comparison is demonstrated using simulated and real data from a ‘stag-hunt’. Finally, we note that exactly the same sophisticated behaviour can be achieved by optimising the utility function itself (through prosocial utility), producing unsophisticated but apparently altruistic agents. This may be relevant ethologically in hierarchal game theory and coevolution.     

Theory of gastric function

On the basis of some assumptions concerning gastric emptying a theory of gastric function is developed which explains the known facts —chiefly the emptying of liquids according to an exponential law. On the basis of this theory an equation is derived which relates the rate of secretion to the quantity of liquid retained in the stomach after a certain time. A study is made of the general characteristics of this equation. Some assumptions concerning different formulae describing the rate of secretion are found useful in experimental investigations, particularly in Hollander’s dilution indicator method.     

Evaluation of Current Population Genetics Theory

My aim is to give a partial evaluation or critique of the stateof population genetics theory. A decent theory must includethe following components: the development of concepts of fitnessthat have demonstrated epistemic correlations, life tables,mating, fecundity, finite (even if large) niche size, and, ofcourse, Mendelism and mutation. It must in the end also includevarying environment and competition between species. The extentto which the desiderata are met is discussed. The big lacunaein the whole theory appear to be the inadequate treatment offitness and the ignoring of niche capacity. Some theorems thatare given as fundamental must be questioned and even discarded.Integration of ideas of simple Mendelism, quantitative geneticvariation, and ecology is the big task ahead. It is criticalthat more complete theory be developed.     

Chemical Organisation Theory

Complex dynamical reaction networks consisting of many components that interact and produce each other are difficult to understand, especially, when new component types may appear and present component types may vanish completely. Inspired by Fontana and Buss (Bull. Math. Biol., 56, 1–64) we outline a theory to deal with such systems. The theory consists of two parts. The first part introduces the concept of a chemical organisation as a closed and self-maintaining set of components. This concept allows to map a complex (reaction) network to the set of organisations, providing a new view on the system’s structure. The second part connects dynamics with the set of organisations, which allows to map a movement of the system in state space to a movement in the set of organisations. The relevancy of our theory is underlined by a theorem that says that given a differential equation describing the chemical dynamics of the network, then every stationary state is an instance of an organisation. For demonstration, the theory is applied to a small model of HIV-immune system interaction by Wodarz and Nowak (Proc. Natl. Acad. USA, 96, 14464–14469) and to a large model of the sugar metabolism of E. Coli by Puchalka and Kierzek (Biophys. J., 86, 1357–1372). In both cases organisations where uncovered, which could be related to functions. Both authors contributed equally.     

Resilience Theory in Archaeology

The past can be characterized by periods of changing and stable relationships between human groups and their environment. In this article, I argue that use of "resilience theory" as a conceptual framework will assist archaeologists in interpreting the past in ways that are interesting and potentially relevant to contemporary issues. Many of the authors in this "In Focus" section primarily concentrate on the relationships associated with patterns of human extraction of resources and the impacts of those human activities on the continuing condition of the ecosystem. These processes are, of course, embedded in a complex web of relationships that are based on multiple interactions of underlying patterns and processes of both the ecological and social domains. In this article, I introduce a resilience theory perspective to argue that these transformations were characterized by very different reorganizations of the socioecological landscape and were the product of a variety of factors that operated at different scales of geography, time, and social organization.     

岛屿生物地理学理论：模型与应用

前言岛屿有许多显著特征,如地理隔离,生物类群简单。这些特点为重复性研究和统计学分析奠定了基础,从而有利于许多深入而细致的生物学研究。因此,岛屿为发展和检验自然选择、物种形成及演化,以及生物地理学和生态学诸领域的理论和假设,提供了重要的自然实验室。岛屿生物地理学理论(MacArthurwilson学说)即为岛屿生物学研究中所产生的著名理论之一。该理论发展之     

The Rapan Theory of Conception

People in Rapa, French Polynesia, attempt to limit their families by abstaining from intercourse during the time they think the woman is most likely to conceive. They have little success with this method of contraception, largely because they believe conception occurs during the three or four days immediately following menstruation. This placement of the fertile period is based on a theory of reproduction quite different from that currently prevailing in the West. The Rapan theory is explained, and other societies holding similar ideas concerning the fertile period are indicated.     

Theory of passive permeability through lipid bilayers

Recently measured water permeability through bilayers of different lipids is most strongly correlated with the area per lipid A rather than with other structural quantities such as the thickness. This paper presents a simple three-layer theory that incorporates the area dependence in a physically realistic way and also includes the thickness as a secondary modulating parameter. The theory also includes the well-known strong correlation of permeability upon the partition coefficients of general solutes in hydrocarbon environments (Overton's rule). Two mathematical treatments of the theory are given; one model uses discrete chemical kinetics and one model uses the Nernst-Planck continuum equation. The theory is fit to the recent experiments on water permeability in the accompanying paper.     

Ecological Theory and Community Restoration Ecology

Community ecological theory may play an important role in the development of a science of restoration ecology. Not only will the practice of restoration benefit from an increased focus on theory, but basic research in community ecology will also benefit. We pose several major thematic questions that are relevant to restoration from the perspective of community ecological theory and, for each, identify specific areas that are in critical need of further research to advance the science of restoration ecology. We ask, what are appropriate restoration endpoints from a community ecology perspective? The problem of measuring restoration at the community level, particularly given the high amount of variability inherent in most natural communities, is not easy, and may require a focus on restoration of community function (e.g., trophic structure) rather than a focus on the restoration of particular species. We ask, what are the benefits and limitations of using species composition or biodiversity measures as endpoints in restoration ecology? Since reestablishing all native species may rarely be possible, research is needed on the relationship between species richness and community stability of restored sites and on functional redundancy among species in regional colonist “pools.” Efforts targeted at restoring system function must take into account the role of individual species, particularly if some species play a disproportionate role in processing material or are strong interactors. We ask, is restoration of habitat a sufficient approach to reestablish species and function? Many untested assumptions concerning the relationship between physical habitat structure and restoration ecology are being made in practical restoration efforts. We need rigorous testing of these assumptions, particularly to determine how generally they apply to different taxa and habitats. We ask, to what extent can empirical and theoretical work on community succession and dispersal contribute to restoration ecology? We distinguish systems in which succession theory may be broadly applicable from those in which it is probably not. If community development is highly predictable, it may be feasible to manipulate natural succession processes to accelerate restoration. We close by stressing that the science of restoration ecology is so intertwined with basic ecological theory that practical restoration efforts should rely heavily on what is known from theoretical and empirical research on how communities develop and are structured over time.     

Differential polarization imaging. I. Theory

A theory of differential polarization imaging is derived using Mueller calculus. It is shown that, for any arbitrary object, 16 images (in general different) can be obtained by combining different incident polarizations of light and measuring the specific polarization components transmitted or scattered by the object. These are called the Mueller images of the object. Mathematical expressions of these images for an object of arbitrary geometry are derived using classical vector diffraction theory and the paraxial and thin lens approximations. The object is described as a collection of point polarizable groups. The electromagnetic fields are calculated using the first Born-Approximation, but extension of the theory to higher-order approximations is shown to be straightforward. These expressions are obtained for the transmission, or bright-field, geometry, and the scattering, or dark-field, configuration. In both cases, the contributions of scattering, absorption, and background illumination to the Mueller images are characterized. The contributions of linear dichroism, circular dichroism, and linear and circular intensity differential scattering to certain Mueller images are established. It is shown that the Mueller images represent a complete two-dimensional mapping of the molecular anisotropy of the object.     

Theory of ameboid movements

A theory of the random change of the shape of an ameba, produced by protusion and retraction of pseudopods is developed on the assumption that a local disturbance, which reduces the surface tension, travels along the surface of the ameba. Quantitative relations suggesting experimental verification are derived for the average size and average duration of a pseudopod.     

Theory of friction-limited DNA unwinding

The theory of friction-limited DNA unwinding is developed explicitly for moderate tind large perturbations. This extension of the earlier theory of the relaxation kinetics is necessary because of the complex nature of the rate limitation for small perturbations. The assumption of the theory that is violated under relaxation conditions is that base pairing reactions occurring at a constant local degree of twist of the strands are fast compared to the net unwinding of the molecule. However, these reactions that are slow for small perturbations have a large activation energy, and become faster than friction-limited un winding for large enough temperature jumps and sufficiently large DXA molecules. Thus only the rate for moderate and large perturbations is clearly limited by frictional resistance to turning the molecule in solution. The model used is a diffusional unwinding of the two strands, driven by the accompanying decrease in free energy. For large perturbations a numerical solution of the diffusion equation is required, since the diffusion coefficient is not constant. Two new parameters must be introduced into the equilibrium statistical theory to describe friction-limited unwinding kinetics. These are the force constant b, for winding up coil regions and the frictional coefficient per base pair β_cfor rotating coil regions in solution. We find by fitting the theory to experiment that b = 1.8 × 10^?13 ergs/ rad²- and β_c = 3.5 × 10^?21 erg see/base pair, both for DNA melted in alkali at 0.4.M Na ⁺ and ～30 °C. The latter value is in agreement with predictions based on the viscosity of single stranded DNA in alkali. The quoted value of bcan be interpreted to mean that the number of conformational states of a nucleolide is reduced by an average factor of 1.55 when it is wound around another strand to the degree of twist in a double helix, but without forming a base pair.     

Application of a Theory for Circumnutations to Geotropic Movements

From a previously published theory (Israelsson and Johnsson 1967) for circumnutations in Helianthus annuus it is possible to predict the geotropical curvatures of the hypocotyls. This extension of the theory is given in the present paper and some geotropical experiments are performed and discussed. The agreement between the theory and the experiments has been verified in the case of gravitational stimulation during relatively short stimulation periods, in the case of continuous gravitational stimulation, etc. Restrictions in the proposed model are discussed.