Astrocladistics: A Phylogenetic Analysis of Galaxy Evolution I. Character Evolutions and Galaxy Histories

This series of papers is intended to present astrocladistics in some detail and evaluate this methodology in reconstructing phylogenies of galaxies. Being based on the evolution of all the characters describing galaxies, it is an objective way of understanding galaxy diversity through evolutionary relationships. In this first paper, we present the basic steps of a cladistic analysis and show both theoretically and practically that it can be applied to galaxies. For illustration, we use a sample of 50 simulated galaxies taken from the GALICS database, which are described by 91 observables (dynamics, masses and luminosities). These 50 simulated galaxies are indeed 10 different galaxies taken at 5 cosmological epochs, and they are free of merger events. The astrocladistic analysis easily reconstructs the true chronology of evolution relationships within this sample. It also demonstrates that burst characters are not relevant for galaxy evolution as a whole. A companion paper is devoted to the formalization of the concepts of formation and diversification in galaxy evolution.     

The MAP test for multimodality

We introduce a test for detecting multimodality in distributions based on minimal constrained spanning trees. We define a Minimal Ascending Path Spanning Tree (MAPST) on a set of points as a spanning tree that has the minimal possible sum of lengths of links with the constraint that starting from any link, the lengths of the links are non-increasing towards a root node. We define similarly MAPSTs with more than one root. We present some algorithms for finding such trees. Based on these trees, we devise a test for multimodality, called the MAP Test (for Minimal Ascending Path). Using simulations, we estimate percentage points of the MAP statistic and assess the power of the test. Finally, we illustrate the use of MAPSTs for determining the number of modes in a distribution of positions of galaxies on photographic plates from a rich galaxy cluster.     

Development (and Evolution) of the Universe

I distinguish Nature from the World. I also distinguish development from evolution. Development is progressive change and can be modeled as part of Nature, using a specification hierarchy. I have proposed a ‘canonical developmental trajectory’ of dissipative structures with the stages defined thermodynamically and informationally. I consider some thermodynamic aspects of the Big Bang, leading to a proposal for reviving final cause. This model imposes a ‘hylozooic’ kind of interpretation upon Nature, as all emergent features at higher levels would have been vaguely and episodically present primitively in the lower integrative levels, and were stabilized materially with the developmental emergence of new levels. The specification hierarchy’s form is that of a tree, with its trunk in its lowest level, and so this hierarchy is appropriate for modeling an expanding system like the Universe. It is consistent with this model of differentiation during Big Bang development to view emerging branch tips as having been entrained by multiple finalities because of the top-down integration of the various levels of organization by the higher levels.     

Towards a Hierarchical Definition of Life,the Organism,and Death

Despite hundreds of definitions, no consensus exists on a definition of life or on the closely related and problematic definitions of the organism and death. These problems retard practical and theoretical development in, for example, exobiology, artificial life, biology and evolution. This paper suggests improving this situation by basing definitions on a theory of a generalized particle hierarchy. This theory uses the common denominator of the “operator” for a unified ranking of both particles and organisms, from elementary particles to animals with brains. Accordingly, this ranking is called “the operator hierarchy”. This hierarchy allows life to be defined as: matter with the configuration of an operator, and that possesses a complexity equal to, or even higher than the cellular operator. Living is then synonymous with the dynamics of such operators and the word organism refers to a select group of operators that fit the definition of life. The minimum condition defining an organism is its existence as an operator, construction thus being more essential than metabolism, growth or reproduction. In the operator hierarchy, every organism is associated with a specific closure, for example, the nucleus in eukaryotes. This allows death to be defined as: the state in which an organism has lost its closure following irreversible deterioration of its organization. The generality of the operator hierarchy also offers a context to discuss “life as we do not know it”. The paper ends with testing the definition’s practical value with a range of examples.     

进化论视域中的道德——恩斯特·迈尔的道德进化思想研究

迈尔对道德的进化问题具有深刻的认识和精致的论证。他对生物利他现象与人类道德行为的关系做了辩证的思考,认为利他现象与道德行为既有密切的联系,又有本质的区别。他从生物进化与文化进化协同的视角研究了道德规范的形成与传递,认为道德规范是后天习得的,但也与遗传下来的倾向和能力有关。他还从进化人道主义立场出发,提出道德规范应该具有的适应性与灵活性。     

将“肝系”一词纳入中医术语体系的建议

探讨中医术语“肝”的起源与演变,可以发现“肝”的“能指/所指”关系发生过多次转移:物质实体→功能概念→物质实体。“肝”的组合关系和聚合关系,揭示了“肝”的意义指向,以及在整个符号系统中的地位。“肝”的隐喻和转喻同样揭示的是组合关系和聚合关系,隐喻的基础是相似,转喻的基础是相近,以此可以说明中医“肝”概念的形成过程。从历时上考察,“肝”的所指存在混乱和边界不清的情况。在目前中医药术语规范体系中,尚缺乏一个重要术语“肝系”。“肝系”一词的使用,具有词频和理据两方面的合理性,且具有较强的区分度和解释功能。“心系”“脾系”“肺系”“肾系”等同级别名词也应相应增加,才符合系统性。     

Complexity and Evolution: A Study of the Growth of Complexity in Organic and Cultural Evolution

In the present paper I develop a model of the evolutionary process associated to the widespread although controversial notion of a prevailing trend of increasing complexity over time. The model builds on a coupling of evolution to individual developmental programs and introduces an integrated view of evolution implying that human culture and science form a continuous extension of organic evolution. It is formed as a mathematical model that has made possible a quantitative estimation in relative terms of the growth of complexity. This estimation is accomplished by means of computer simulations the result of which indicates a strong acceleration of complexity all the way from the appearance of multicellular organisms up to modern man.     

译介术语演化分析

针对中国译介研究术语演化规律这一科学问题,采用文献计量方法对中国期刊全文数据库(1963—2016)中的译介研究关键词进行了统计分析。结果表明中国译介研究术语经历了三个演化阶段:第一阶段为1963—1982年,这期间相关研究论文的数量比较稀少,导致术语贫乏;第二阶段为1983—2000年,这期间发文量明显增多,多研究重心开始形成,新的术语不断产生;第三阶段为2001—2016年,这期间发文量大规模增长,研究重心发生迁移,术语呈现“百花齐放”态势。当前,中国译介研究方兴未艾,译介研究术语更多地被赋予了时代性、民族性、多样性的文化内涵。     

Studies on Molecular Mechanisms of Prebiotic Systems

Lately there has been a growing interest in evolutionary studies concerning how the regularities and patterns found in the living cell could have emerged spontaneously by way of self-assembly and self-organization. It is reasonable to postulate that the chemical compounds found in the primitive Earth would have mostly been very simple in nature, and would have been immersed in the natural dynamics of the physical world, some of which would have involved self-organization. It seems likely that some molecular processes self-organized spontaneously into a hierarchy of complex behaviours. Our conceptual search herein reaches back to the time when prebiotic phenomena began to take shape. This was before the origin of life, so in this paper we hope to shed new light on some of the theoretical issues that surround the ways in which cellular organization might have evolved without the aid of replicated information.     

On Gene’s Action and Reciprocal Causation

Advancing the reductionist conviction that biology must be in agreement with the assumptions of reductive physicalism (the upward hierarchy of causal powers, the upward fixing of facts concerning biological levels) A. Rosenberg argues that downward causation is ontologically incoherent and that it comes into play only when we are ignorant of the details of biological phenomena. Moreover, in his view, a careful look at relevant details of biological explanations will reveal the basic molecular level that characterizes biological systems, defined by wholly physical properties, e.g., geometrical structures of molecular aggregates (cells). In response, we argue that contrary to his expectations one cannot infer reductionist assumptions even from detailed biological explanations that invoke the molecular level, as interlevel causal reciprocity is essential to these explanations. Recent very detailed explanations that concern the structure and function of chromatin—the intricacies of supposedly basic molecular level—demonstrate this. They show that what seem to be basic physical parameters extend into a more general biological context, thus rendering elusive the concepts of the basic level and causal hierarchy postulated by the reductionists. In fact, relevant phenomena are defined across levels by entangled, extended parameters. Nor can the biological context be explained away by basic physical parameters defining molecular level shaped by evolution as a physical process. Reductionists claim otherwise only because they overlook the evolutionary significance of initial conditions best defined in terms of extended biological parameters. Perhaps the reductionist assumptions (as well as assumptions that postulate any particular levels as causally fundamental) cannot be inferred from biological explanations because biology aims at manipulating organisms rather than producing explanations that meet the coherence requirements of general ontological models. Or possibly the assumptions of an ontology not based on the concept of causal powers stratified across levels can be inferred from biological explanations. The incoherence of downward causation is inevitable, given reductionist assumptions, but an ontological alternative might avoid this. We outline desiderata for the treatment of levels and properties that realize interlevel causation in such an ontology.     

WTO视角下我国有效金融市场与企业经营多元化的研究

本文分析有效市场假说和企业多元化的经营动机，探求金融市场演变的不同形态及其有效程度。以及其对社会资源的分配功能的影响，揭示金融市场不同的有效程度与多元化企业经营的战略选择的内在关系。在此基础上，研究我国企业经营多元化的问题和对策，具有突出的理论和现实意义。     

Explaining the Origin of Life is not Enough for a Definition of Life

The comments focus on a presumed circular reasoning in the operator hierarchy and the necessity of understanding life’s origin for defining life. Below it is shown that its layered structure prevents the operator hierarchy from circular definitions. It is argued that the origin of life is an insufficient basis for a definition of life that includes multicellular and neural network organisms.     

学术论文与技术专利:鱼与熊掌能否兼得?

运用负二项回归模型研究了论文与专利的关系及其影响因素。论文数量与专利数量之间存在双向的"倒U型"关系。纵向项目不仅对论文数量和专利数量具有直接影响,而且通过专利或论文的中介效应产生间接影响。横向项目对论文数量和专利数量都没有显著影响。单位等级和单位类别对论文与专利的关系具有显著的调节效应。年龄、第一学历、最后学位等因素也对论文数量、专利数量具有一定的影响。     

我国宋代牡丹品种和数目的再研究

宋代是我国古代牡丹品种的研究、培育和数目发展较快的一个时期。宋代牡丹品种的数目,《天彭牡丹谱》（陆游,１１７８年）认为约有百个;该文比较研究了现存的一些宋代牡丹著作,经综合整理后提出有１９１个。这一数字更充分地证实我国乃是牡丹栽培品种分化、演变和多样性的古老中心。     

我国传统学科术语外译研究:回顾、反思与展望

术语是一门学科理论的核心和灵魂,是对外交流和传播的核心要素。近二十年来,中国传统学科术语外译研究取得了显著的成绩,无论是理论研究还是应用研究都呈现出理论多样化、视角个性化、方法多元化、范围扩大化以及注重文化内涵的深层阐释和传播的发展趋势。但从研究现状来看,仍然存在一些问题。未来还应进一步提高翻译本体研究的系统性,注重翻译规范和翻译方法的整合性,突破翻译主体的局限性,从而促进我国传统学科对外传播。     

自然选择是万能的吗?——进化论中的适应主义及其生物学哲学争论

自然选择是达尔文进化论学说的重要概念。达尔文之后,关于自然选择的作用,形成了两种互相对立的学说:适应主义和反适应主义。适应主义者认为,自然选择是万能的,生物的进化都是通过自然选择而获得适应性进化的结果;反适应者主义者则认为,自然选择的作用不是万能的,生物还可以通过其他途径进化。鉴于适应主义的广泛影响及其在理解进化生物学中的重要作用,本文拟澄清适应主义的含义及其形式,阐明适应主义与反适应主义在生物学和哲学两个层面的争论,并指出适应主义思想的局限性及多元主义视角的价值。     

Preserving consensus hierarchies

In numerical taxonomy we often have the task of finding a consensus hierarchy for a given set of hierarchies. This consensus hierarchy should reflect the substructures which are common to all hierarchies of the set. Because there are several kinds of substructures in a hierarchy, the general axiom to preserve common substructures leads to different axioms for each kind of substructure. In this paper we consider the three substructurescluster, separation, andnesting, and we give several characterizations of hierarchies preserving these substructures. These characterizations facilitate interpretation of axioms for preserving substructures and the examination of properties of consensus methods. Finally some extensions concerning the preserving of qualified substructures are discussed.The author is grateful to the editor and the referees for their helpful suggestions and to H. J. Bandelt for his comments on an earlier version of this paper.     

Directed Binary Hierarchies and Directed Ultrametrics

Directed binary hierarchies have been introduced in order to give a graphical reduced representation of a family of association rules. This type of structure extends the classical binary hierarchical classification in a very specific way. In this paper an accurate formalization of this new structure is studied. A directed hierarchy is defined as a set of ordered pairs of subsets of the initial individual set satisfying specific conditions. A new notion of directed ultrametricity is studied. The main result consists in establishing a bijective correspondence between a directed ultrametric space and a directed binary hierarchy. Finally, an algorithm is proposed in order to transform a directed ultrametric structure into a graphical representation associated with a directed binary hierarchy.     

现代科学的复杂性审视--齐曼科学社会学思想的新发展

约翰·齐曼是一位科学家出身的科学社会学家。他认为现代科学正在从学院时代走向了后学院时代,因此其传统的学术规范即默顿规范随之也要作出相应的修正;科学进步也像生物进化,有自然选择但也有自组织能力;科学虽然并不具有绝对可靠性,但它仍然有理由值得我们去信赖。     

一个快速进化的microRNA家族

microRNAs(miRNAs)是长约22nt的非编码RNA,它可通过降解mRNA或抑制其翻译来调控基因。本文简要介绍了miRNAs的研究背景,阐述了通过比较近缘物种中非保守的miRNA基因来研究miRNAs分子进化的理由。我们的研究结果证实miRNA基因会受到达尔文正选择的影响,发生快速的进化。这一结果将为我们了解非蛋白编码基因的功能与进化提供崭新的视角。