Stretch Coding and Block Coding: Two New Strategies to Represent Questionably Aligned DNA Sequences

Most coding strategies that address the problem of questionable alignment (elision, case sensitive, missing, polymorphic, gaps as presence/absence matrix) conflict with phylogenetic principles, particularly those relating to the concept of homology (shared similiarity explained by common ancestry). In some cases, the test of conjunction is failed. In other cases, characters that are coded ambiguously can lead to character-state optimization in the terminal taxa that conflicts with the original observations. Only data exclusion and contraction avoid these pitfalls. In highly dissimilar sequences additional character states can represent the available information. Two new methods that accomplish this—block and stretch coding—are introduced here. These two new coding strategies are not in conflict with the test of conjunction and do not contradict the original observations. They are comparable to coding practices with morphological data once the intrinsic differences due to character-state identity and topographical identity have been taken into account. It is suggested that, of the three recoding methods, the one is selected that preserves the maximum potential phylogenetic information as measured with the minimum number of steps required for the particular part of the data matrix. Received: 1 August 2000 / Accepted: 10 July 2001     

Coordinated Optimization of Visual Cortical Maps (I) Symmetry-based Analysis

In the primary visual cortex of primates and carnivores, functional architecture can be characterized by maps of various stimulus features such as orientation preference (OP), ocular dominance (OD), and spatial frequency. It is a long-standing question in theoretical neuroscience whether the observed maps should be interpreted as optima of a specific energy functional that summarizes the design principles of cortical functional architecture. A rigorous evaluation of this optimization hypothesis is particularly demanded by recent evidence that the functional architecture of orientation columns precisely follows species invariant quantitative laws. Because it would be desirable to infer the form of such an optimization principle from the biological data, the optimization approach to explain cortical functional architecture raises the following questions: i) What are the genuine ground states of candidate energy functionals and how can they be calculated with precision and rigor? ii) How do differences in candidate optimization principles impact on the predicted map structure and conversely what can be learned about a hypothetical underlying optimization principle from observations on map structure? iii) Is there a way to analyze the coordinated organization of cortical maps predicted by optimization principles in general? To answer these questions we developed a general dynamical systems approach to the combined optimization of visual cortical maps of OP and another scalar feature such as OD or spatial frequency preference. From basic symmetry assumptions we obtain a comprehensive phenomenological classification of possible inter-map coupling energies and examine representative examples. We show that each individual coupling energy leads to a different class of OP solutions with different correlations among the maps such that inferences about the optimization principle from map layout appear viable. We systematically assess whether quantitative laws resembling experimental observations can result from the coordinated optimization of orientation columns with other feature maps.     

The Precautionary Principle and Marine Environmental Protection: Slippery Shores,Rough Seas,and Rising Normative Tides

Law and policy implications of the precautionary principle in the field of marine environmental protection are explored in this paper in a three-part analysis. First, seven slippery aspects of the precautionary principle are highlighted, including confusion in terminology, definitional variations, definitional generalities, the spectrum of precautionary measures available, ongoing philosophical tensions and competing socioeconomic interests, debate over who should be responsible for making precautionary decisions, and limited interpretation by international tribunals. Second, the rather feeble precautionary responses to the tempestuous issues of climate change, hazardous chemicals, and overfishing are described. Third, the potential for the precautionary principle to synergize with human rights norms, such as the emerging right to a healthy environment, and other principles of sustainable development is discussed.     

General generative principles

In search of general generative principles I start from the postulate of a reality which comprises both materialistic and psychic aspects. This overall reality, described by others as the world of archetypes, is not directly accessible to sensory perception. Yet, by studying archetypical manifestations, it is possible to distinguish different structures or generative principles in it. Comparison of three models, which depict developmental processes in different disciplines, shows that they have the same basic structure. The effects of the archetypes involved can be described as four general generative principles: 1st the principle of wholeness (connection and integration of conflicting opposites), 2nd the principle of complementation and compensation (periodic change of opposite influences); 3rd the enstructuring principle (relative stability or spatial aspect of a manifest structure), and 4th the principle of gesture (change or temporal aspect of that structure).     

Free riders and pious sons--why science research remains obligatory

John Harris has previously proposed that there is a moral duty to participate in scientific research. This concept has recently been challenged by Iain Brassington, who asserts that the principles cited by Harris in support of the duty to research fail to establish its existence. In this paper we address these criticisms and provide new arguments for the existence of a moral obligation to research participation. This obligation, we argue, arises from two separate but related principles. The principle of fairness obliges us to support the social institutions which sustain us, of which research is one; while the principle of beneficence, or the duty of rescue, imposes upon us a duty to prevent harm to others, including by supporting potentially beneficial, even life-saving research. We argue that both these lines of argument support the duty to research, and explore further aspects of this duty, such as to whom it is owed and how it might be discharged.     

Direction change of plant root growth by the impenetrable boundary

Spatial boundary conditions must be considered when utilizing mathematical modeling of plant root growth in the container or along with the imbedding solid obstacle. Using basic root growth principles and the geometry of the boundary surface, a mathematical model can be designed to keep all root elements inside the container or outside the obstacle without passing through the boundary after the minimum deflection of growth direction, and it is based on the minimum friction between root tips and soil and energy saving principles. Such a mathematical method is used to simulate the spatial distribution of root growth and the morphological architecture of the root system near the boundary. The validity of this model is supported by experimental observations that confirm some typical characteristics predicted by the simulations. This model can be widely used in resolving boundary condition complications where water and nutrients are consumed by plants in a spatially limited or heterogeneous resource field.     

Complex multicellularity in fungi: evolutionary convergence,single origin,or both?

Complex multicellularity represents the most advanced level of biological organization and it has evolved only a few times: in metazoans, green plants, brown and red algae and fungi. Compared to other lineages, the evolution of multicellularity in fungi follows different principles; both simple and complex multicellularity evolved via unique mechanisms not found in other lineages. Herein we review ecological, palaeontological, developmental and genomic aspects of complex multicellularity in fungi and discuss general principles of the evolution of complex multicellularity in light of its fungal manifestations. Fungi represent the only lineage in which complex multicellularity shows signatures of convergent evolution: it appears 8–11 times in distinct fungal lineages, which show a patchy phylogenetic distribution yet share some of the genetic mechanisms underlying complex multicellular development. To explain the patchy distribution of complex multicellularity across the fungal phylogeny we identify four key observations: the large number of apparently independent complex multicellular clades; the lack of documented phenotypic homology between these clades; the conservation of gene circuits regulating the onset of complex multicellular development; and the existence of clades in which the evolution of complex multicellularity is coupled with limited gene family diversification. We discuss how these patterns and known genetic aspects of fungal development can be reconciled with the genetic theory of convergent evolution to explain the pervasive occurrence of complex multicellularity across the fungal tree of life.     

Relation of branching angles to optimality for four cost principles

The literature has suggested that branching angles depend on some principle of optimality. Most often cited are the minimization of lumen surface, volume, power and drag. The predicted angles depend on the principle applied, chi and alpha. Assuming flow o r chi, chi can be determined from r chi 0 = r chi 1 + r chi 2 when the radii of the parent (r0) major (r1) and minor (r2) daughters are known. The term alpha = r2/r1. Using different values for chi and alpha, we present graphs for the major and minor branching angles theta 1 and theta 2 and psi = theta 1 + theta 2 for each of the four optimization principles. Because psi is almost independent of alpha for values of chi and alpha found in 198 junctions taken from a human pulmonary artery, we are able to produce a plot of psi versus chi for each of the four principles on one graph. A junction can be provisionally classified as optimizing for a given principle if, knowing chi, the psi obs - psi pred is least for that principle. We find that this nomographic classification agrees almost perfectly with a previous classification based on a more exacting measure, the percent cost index I, where I = observed cost/minimum cost. We explain why this is to be expected in most but not all cases. First we generate a contoured percent cost surface of c = I - 100 around the optimally located junction, J, and superimpose a surface of equal angular deviations a = psi pred-psi obs. We find that c increases and a usually increases with distance from J as the actual junction moves along a straight line away from J. We then produce a plot of c versus a for two competing principles. A comparison of the principles demonstrates that, for most cases, a is smaller for the principle which has the smaller c value.     

First,do no harm: Generalized procreative non‐maleficence

New reproductive technologies allow parents some choice over their children. Various moral principles have been suggested to regulate such choices. This article starts from a discussion of Julian Savulescu's Principle of Procreative Beneficence (PPB), according to which parents ought to choose the child expected to have the best quality of life, before combining two previously separate lines of attack against this principle. First, it is suggested that the appropriate moral principles of guiding reproductive choices ought to focus on general wellbeing rather than prioritizing that of the child and, second, that they ought to be non‐maximizing (e.g. seeking the ‘good enough’ or to avoid harm). Though neither of these suggestions is entirely novel, combining them results in a new, and arguably more plausible, principle to regulate procreative choices, which I call the Principle of Generalized Procreative Non‐Maleficence (PGPNM). According to this principle, the primary obligation on parents is not to cause harm to other people through their reproductive choices.     

Methodological Problems in Evolutionary Biology. XII. Against Evolutionary Ethics

Evolutionary ethics has recently become popular again. Some of its representatives elaborate new attempts to derive ethics from evolutionary biology. The attempts, like previous ones, fail because they commit the naturalistic fallacy. Premises from evolutionary biology together with normative premises also do not justify ethical principles. Other representatives argue that evolutionary considerations imply that ethics cannot be justified at all. Their arguments presuppose an unacceptable form of foundationalism. In principle, evolutionary biology might explain some aspects of morality, but in practice explanations are hard to come by. All this does not imply that evolutionary theory is irrelevant in normative settings. To the contrary, it may help us devise guidelines in environmental policy and health care policy. It is to be hoped that evolutionary ethicists will divert their research efforts to the elaboration of such guidelines.     

Biomechanical model of the xylem vessels in vascular plants

BACKGROUND AND AIMS: The xylem, or water transport system, in vascular plants adopts different morphologies that appear sequentially during growth phases. This paper proposes an explanation of these morphologies based on engineering design principles. METHODS: Using microscopic observations of the different growth stages, an engineering analysis of the xylem vessels as a closed cylinder under internal pressure is carried out adopting pressure vessel design concepts. KEY RESULTS: The analysis suggests that the xylem vessel structural morphology follows the 'constant strength' design principle, i.e. all of the material within the wall of the xylem is loaded equally to its maximum allowable stress capacity, and the amount of material used is therefore systematically minimized. The analysis shows that the different structural designs of the xylem vessel walls (annular, helical, reticulate and pitted) all quantitatively follow the constant strength design principle. CONCLUSIONS: The results are discussed with respect to growth and differentiation. It is concluded that the morphology of the xylem vessel through the different phases of growth seems to follow optimal engineering design principles.     

Computer modeling of fibrin polymerization kinetics correlated with electron microscope and turbidity observations: clot structure and assembly are kinetically controlled.

Although much is known about fibrin polymerization, because it is complex, the effects of various modifications are not intuitively obvious and many experimental observations remain unexplained. A kinetic model presented here that is based on information about mechanisms of assembly accounts for most experimental observations and allows hypotheses about the effects of various factors to be tested. Differential equations describing the kinetics of polymerization were written and then solved numerically. The results have been related to turbidity profiles and electron microscope observations. The concentrations of intermediates in fibrin polymerization, and fiber diameters, fiber and protofibril lengths have been calculated from these models. The simplest model considered has three steps; fibrinopeptide A cleavage, protofibril formation, and lateral aggregation of protofibrils to form fibers. The average number of protofibrils per fiber, which is directly related to turbidity, can be calculated and plotted as a function of time. The lag period observed in turbidity profiles cannot be accurately simulated by such a model, but can be simulated by modifying the model such that oligomers must reach a minimum length before they aggregate. Many observations, reported here and elsewhere, can be accounted for by this model; the basic model may be modified to account for other experimental observations. Modeling predicts effects of changes in the rate of fibrinopeptide cleavage consistent with electron microscope and turbidity observations. Changes only in the rate constants for initiation of fiber growth or for addition of protofibrils to fibers are sufficient to account for a wide variety of other observations, e.g., the effects of ionic strength or fibrinopeptide B removal or thrombospondin. The effects of lateral aggregation of fibers has also been modeled: such behavior has been observed in turbidity curves and electron micrographs of clots formed in the presence of platelet factor 4. Thus, many aspects of clot structure and factors that influence structure are directly related to the rates of these steps of polymerization, even though these effects are often not obvious. Thus, to a large extent, clot structure is kinetically determined.     

Variational Principles in the Mechanics of Conformational Motions of Macromolecules in a Viscous Medium

The mechanics of the conformational motions of macromolecules due to rotations around the valence bonds in a viscous medium have been considered. The variational principles for the energy-dissipation rate during conformational motions in a viscous medium and the rate of the potential energy decrease of a macromolecule during conformational relaxation have been analyzed. The seeming contradiction between this principle and the principle of the minimum energy-dissipation rate is resolved. It is shown that the energy-dissipation rate must be optimal and minimal in order to simultaneously satisfy the conservation laws and fulfill the deterministic nature of classical trajectories. The generalization and analysis of the influence of thermal fluctuations and external forces on the variational principles for the conformational relaxation of macromolecules is carried out. A visual graphical geometric depiction has been developed using hyperspheres in the space of the velocities of chain nodes to describe conformational movements along many degrees of freedom in a viscous medium. The equipartition of the energy-dissipation rates (and the rates of potential energy decrease) among the conformational degrees of freedom is discussed.     

Biological constraints on orthographic representation

This paper sets out five constraints that a psychologically efficient orthography must meet. The first four principles are that (1) the elements of the orthography must be easy to discriminate; (2) it must be possible to write the code quickly, without elaborate technology; (3) the code must permit unambiguous, fast and fail-safe access to the meanings of messages; (4) the system as a whole should be learnable without undue expenditure of time and effort. A fifth principle, that the dimensions of formal and semantic similarity in an orthography should be orthogonal, is argued to be the best way of ensuring that reading errors are kept to a minimum. Evidence for the last principle is derived from the study of errors made by subjects with acquired dyslexia.     

配额目标约束下区域减排的最优控制率

研究了区域碳排放配额目标给定下,如何确定一个保障经济平稳增长的最优碳排放控制率问题。提出了一个最优减排率确定的计算流程,并且根据前瞻性原则、人口原则、GDP原则、GDP-人口原则、支付能力原则5种不同的碳排放配额分配原则,确定了中国大部分省市自治区可能的最优减排率。选取5个中国省区上海、山西,湖南、云南以及新疆作为案例地区,在计算得到这些地区的减排率的约束下,分析了在社会福利最大化的情况下各区域分配的配额获得的经济增长路径和能源碳排放路径。模拟结果发现,中国在各种减排约束下各区域的经济增长路径呈阶梯式下降的趋势。能源碳排放呈先升后降的整体趋势,各个省市自治区要实现2030年后不再增加碳排放。得出各东部省份在GDP原则分配的配额约束下减排控制率最小,西部省份在支付能力原则下减排控制率最小,而中部省份则在人口原则下减排控制率较小。5个原则中前瞻性原则适合中国推进的碳减排配额方法。     

Self-Determination vs. Family-Determination: Two Incommensurable Principles of Autonomy

Most contemporary bioethicists believe that Western bioethical principles, such as the principle of autonomy, are universally binding wherever bioethics is found. According to these bioethicists, these principles may be subject to culturally-conditioned further interpretations for their application in different nations or regions, but an 'abstract content' of each principle remains unchanged, which provides 'an objective basis for moral judgment and international law'. This essay intends to demonstrate that this is not the case. Taking the principle of autonomy as an example, this essay argues that there is no such shared 'abstract content' between the Western bioethical principle of autonomy and the East Asian bioethical principle of autonomy. Other things being equal, the Western principle of autonomy demands self-determination, assumes a subjective conception of the good and promotes the value of individual independence, whilst the East Asian principle of autonomy requires family-determination, presupposes an objective conception of the good and upholds the value of harmonious dependence. They differ from each other in the most general sense and basic moral requirement.     

Self-determination vs. family-determination: two incommensurable principles of autonomy: a report from East Asia

Most contemporary bioethicists believe that Western bioethical principles, such as the principle of autonomy, are universally binding wherever bioethics is found. According to these bioethicists, these principles may be subject to culturally-conditioned further interpretations for their application in different nations or regions, but an 'abstract content' of each principle remains unchanged, which provides 'an objective basis for moral judgment and international law'. This essay intends to demonstrate that this is not the case. Taking the principle of autonomy as an example, this essay argues that there is no such shared 'abstract content' between the Western bioethical principle of autonomy and the East Asian bioethical principle of autonomy. Other things being equal, the Western principle of autonomy demands self-determination, assumes a subjective conception of the good and promotes the value of individual independence, whilst the East Asian principle of autonomy requires family-determination, presupposes an objective conception of the good and upholds the value of harmonious dependence. They differ from each other in the most general sense and basic moral requirement.     

The evolution of Kraepelin's nosological principles

Emil Kraepelin developed a new psychiatric nosology in the eight editions of his textbook. Previous papers have explored his construction of particular diagnoses, including dementia praecox and manic‐depressive insanity. Here we are providing a close reading of his introductory textbook chapter, that presents his general principles of nosology. We identify three phases: 1) editions 1‐4, in which he describes nosological principles in search of data; 2) editions 5‐7, in which he declares the mature version of his nosological principles and develops new disease categories; 3) edition 8, in which he qualifies his nosological claims and allows for greater differentiation of psychiatric disorders. We propose that Kraepelin's nosology is grounded in three principles. First, psychiatry, like other sciences, deals with natural phenomena. Second, mental states cannot be reduced to neural states, but science will progress and will, ultimately, reveal how nature creates abnormal mental states and behavior. Third, there is a hierarchy of validators of psychiatric diagnoses, with the careful study of clinical features (signs, symptoms and course) being more important than neuropathologic and etiological studies. These three principles emerged over the course of the eight editions of Kraepelin's textbook and were informed by his own research and by available scientific methods. His scientific views are still relevant today: they have generated and, at the same time, constrained our current psychiatric nosology.     

Canonical profiles in tokamak plasmas with an arbitrary cross section

Two principles are used to determine a canonical profile: the principle of the minimum of free plasma energy with the constraint that the total current is conserved and the principle of profile consistency. A second-order differential equation for the canonical profile of the function μ=1/q is deduced in the natural coordinate system. Soft and hard boundary conditions are proposed to find an unambiguous solution to this equation. The range of their applicability is discussed. Numerical calculations show that the half-width of the canonical profile increases with decreasing aspect ratio, increasing plasma elongation, and decreasing q _a value. The canonical profiles obtained make it possible to determine the critical gradients for the heat and particle fluxes in transport models.