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。     

Understanding Natural Science Based on Abductive Inference: Continental Drift

This study aims to understand scientific inference for the evolutionary procedure of Continental Drift based on abductive inference, which is important for creative inference and scientific discovery during problem solving. We present the following two research problems: (1) we suggest a scientific inference procedure as well as various strategies and a criterion for choosing hypotheses over other competing or previous hypotheses; aspects of this procedure include puzzling observation, abduction, retroduction, updating, deduction, induction, and recycle; and (2) we analyze the “theory of continental drift” discovery, called the Earth science revolution, using our multistage inference procedure. Wegener’s Continental Drift hypothesis had an impact comparable to the revolution caused by Darwin’s theory of evolution in biology. Finally, the suggested inquiry inference model can provide us with a more consistent view of science and promote a deeper understanding of scientific concepts.     

生物炼制细胞工厂的科学基础

生物炼制是以生物可再生资源为原料生产能源与化工产品的新型工业模式。认识并利用微生物广泛的物质分解转化与卓越的化学合成能力,将微生物改造成为高效的生物炼制细胞工厂,使生物炼制逐步取代传统石油炼制,对于降低化石资源消耗、最终实现工业原材料来源的战略大转移、促进经济社会的可持续发展具有重要意义。本文分析了构建生物炼制细胞工厂亟待解决的关键问题,介绍了有关生物炼制细胞工厂的国内外最新研究进展,并对生物炼制细胞工厂的发展前景进行了展望。作为工业生物技术的核心支撑技术之一,生物炼制细胞工厂必将在解决资源、能源问题中起到重要作用。     

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.     

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.     

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.     

What is Information?

The main aim of this work is to contribute tothe elucidation of the concept of informationby comparing three different views about thismatter: the view of Fred Dretske's semantictheory of information, the perspective adoptedby Peter Kosso in his interaction-informationaccount of scientific observation, and thesyntactic approach of Thomas Cover and JoyThomas. We will see that these views involvevery different concepts of information, eachone useful in its own field of application. This comparison will allow us to argue in favorof a terminological `cleansing': it is necessaryto make a terminological distinction among thedifferent concepts of information, in order toavoid conceptual confusions when the word`information' is used to elucidate relatedconcepts as knowledge, observation orentropy.     

“真”是否有本质——基于真理符合论与紧缩论的比较

传统意义上的真之符合论把"真"理解为思想与世界的关系,强调"真"的属性与作用;真之紧缩论则以真的透明性为直觉,涵盖了包括弗雷格紧缩思想、冗余论、代语句理论和极小主义理论在内的几种理论,这些理论的核心思想认为真谓词仅仅起着逻辑句法作用,它的出现不能给语句增添任何实体属性。于是,"真是否有本质"成为符合论与紧缩论争论的焦点,这一争论也成为区分不同真之理论的新标准。     

鲍尔格曼的技术实践思想研究

鲍尔格曼的技术哲学已经得到国内学者很大的关注。但人们主要关注焦点物、设备范式等主要概念的介绍。我们认为,从实践的角度探讨其技术思想应该是一种较新颖的尝试。我们首先关注鲍尔格曼对技术与科学、理论的关系的研究;其次讨论设备范式的概念和当代技术的特点;最后,通过研究焦点物和焦点实践等概念分析其技术实践思想的脉络。在结论中,我们将总结鲍尔格曼的技术的焦点实践思想的主要观点和启示。     

The Meaning of Life in a Developing Universe

The evolution of life on Earth has produced an organism that is beginning to model and understand its own evolution and the possible future evolution of life in the universe. These models and associated evidence show that evolution on Earth has a trajectory. The scale over which living processes are organized cooperatively has increased progressively, as has its evolvability. Recent theoretical advances raise the possibility that this trajectory is itself part of a wider developmental process. According to these theories, the developmental process has been shaped by a yet larger evolutionary dynamic that involves the reproduction of universes. This evolutionary dynamic has tuned the key parameters of the universe to increase the likelihood that life will emerge and produce outcomes that are successful in the larger process (e.g. a key outcome may be to produce life and intelligence that intentionally reproduces the universe and tunes the parameters of ‘offspring’ universes). Theory suggests that when life emerges on a planet, it moves along this trajectory of its own accord. However, at a particular point evolution will continue to advance only if organisms emerge that decide to advance the developmental process intentionally. The organisms must be prepared to make this commitment even though the ultimate nature and destination of the process is uncertain, and may forever remain unknown. Organisms that complete this transition to intentional evolution will drive the further development of life and intelligence in the universe. Humanity’s increasing understanding of the evolution of life in the universe is rapidly bringing it to the threshold of this major evolutionary transition.     

构建建筑学科概念体系的思考

精确、完备、系统的概念体系是学科良好发展的重要根基。长久以来,建筑学科存在着基本范畴不清晰、核心概念不明确、概念定义模糊、概念关系不明、概念未成体系、概念使用混乱等问题,影响了学科的高质量发展、精细化研究以及与其他学科的交流借鉴,也给广大建筑教育者和学习者带来诸多困扰。文章运用聚类思维,将建筑学科本体范畴的最本质、最重要、最稳定、最普遍的概念汇总,按照“建筑本体要素、建筑影响要素、建筑构成要素”的逻辑,对概念进行分析、比较、分类,形成较为系统化的概念和术语体系。通过概念体系的构建,旨在加强建筑学科领域概念使用的精确性与规范性,提升学科理论知识表达的科学性与严谨性,形成对建筑学科的整体、清晰认识,从而促进学科走向成熟、系统和科学。     

血吸虫基因组及疫苗的研究进展

血吸虫病是对人类健康危害最为严重的寄生虫病之一。控制并消灭血吸虫病的危害一直是我国和国际社会的主要目标。近几年来,随着对血吸虫生物学(包括基因组和蛋白质组学)和血吸虫病分子病理学、分子免疫学研究的逐渐开展,血吸虫与哺乳动物宿主(包括人)相互作用及致病的机理不断被揭示。此外,曼氏血吸虫和日本血吸虫的基因组序列已经基本测定完成。对基因组序列的解析不仅能够在遗传学水平上揭示虫体的活动规律,而且还将有利于发现新的药物作用靶位和疫苗抗原。通过对曼氏血吸虫和日本血吸虫基因转录谱和蛋白质表达谱的研究,已经发现了一些血吸虫与宿主相互作用的重要分子(如免疫调节因子及表面黏附蛋白等)。同时,在抗血吸虫疫苗的研究方面也取得了很大的进展,以谷胱苷肽-S-转移酶作为主要抗原的曼氏血吸虫疫苗已经开始I和II期临床试验。此外,多种日本血吸虫抗原也开始在动物体上进行免疫及攻虫试验。本文主要就近年来血吸虫基因组学、蛋白质组学及疫苗研究进展做一概述,同时对相关领域的发展提出展望。     

生物质的抗降解性及其生物炼制中的科学问题

木质纤维素资源的化学成分和结构复杂,目前还缺少能够破坏纤维素结构稳定性的低成本技术,生物降解转化的效率还不能适应大规模工业化要求。国内这方面基础研究相对薄弱,急需针对生物质抗降解屏障与生物转化的难点,围绕其中3个关键科学问题开展研究：（1）植物生物质是如何抗生物降解的——从生物降解转化的角度深入研究这一系列抗性屏障的特性,寻求破解之道,是实现生物质高效转化的基础;（2）微生物是如何攻击植物生物质抗降解屏障的——深入研究微生物降解木质纤维素的机理、多样性以及酶系合成调控,探寻人工构建低成本且高效的复合酶系的可能途径;（3）破解抗性屏障和提高转化效率的可能途径——分子生物学和系统生物学研究的发展为生物的定向设计与改造提供了可能,通过设计和改造植物、微生物及其降解酶系,选育适于转化纤维素为大宗平台化合物的微生物,研究其代谢调控,构建代谢工程菌,研究定向转化的过程及相关产品,结合物理化学预处理技术的研究,可望集成和设计出新的木质纤维素类生物质生物转化液体燃料和化学品的综合生物炼制技术方案。     

How to Get It. Diagrammatic Reasoning as a Tool of Knowledge Development and its Pragmatic Dimension

Discussions concerning belief revision, theorydevelopment, and ``creativity' in philosophy andAI, reveal a growing interest in Peirce'sconcept of abduction. Peirce introducedabduction in an attempt to providetheoretical dignity and clarification to thedifficult problem of knowledge generation. Hewrote that ``An Abduction is Originary inrespect to being the only kind of argumentwhich starts a new idea' (Peirce, CP 2.26).These discussions, however, led to considerabledebates about the precise way in which Peirce'sabduction can be used to explain knowledgegeneration (cf. Magnani, 1999; Hoffmann, 1999).The crucial question is that of understandinghow we can get the new elements capableof enlarging our theories. Under thesecircumstances, it might be helpful to step outof the entanglement and reconsider the basis ofthe problem that originally triggered Peirce'sinterest in abduction. This will lead us toanother Peircean concept, that of ``diagrammaticreasoning,' which I discuss here in the contextof his ``pragmatism.' In this way, I hope toreach a better understanding of thecontribution of ``abduction' to the knowledgegeneration process.     

Mathematics,Philosophical and Semantic Considerations on Infinity (II): Dialectical Vision

Human language has the characteristic of being open and in some cases polysemic. The word “infinite” is used often in common speech and more frequently in literary language, but rarely with its precise meaning. In this way the concepts can be used in a vague way but an argument can still be structured so that the central idea is understood and is shared with to the partners. At the same time no precise definition is given to the concepts used and each partner makes his own reading of the text based on previous experience and cultural background. In a language dictionary the first meaning of “infinite” agrees with the etymology: what has no end. We apply the word infinite most often and incorrectly as a synonym for “very large” or something that we do not perceive its completion. In this context, the infinite mentioned in dictionaries refers to the idea or notion of the “immeasurably large” although this is open to what the individual’s means by “immeasurably great.” Based on this linguistic imprecision, the authors present a non Cantorian theory of the potential and actual infinite. For this we have introduced a new concept: the homogon that is the whole set that does not fall within the definition of sets established by Cantor.     

群体选择论的预先假定

关于选择层次的一个主要问题是:群体选择概念在解释诸如利他行为这类性状的进化中是否必要?目前,这一争论主要是在还原论和基因决定论的框架内进行的。按照这种预先假定,群体选择论主要是用个体的平均性状或者某类性状个体的密度来定义群体特征,从而不能给出具有独立于个体意义的群体概念。这样,所谓选择层次就成了一种约定。近来已经有学者表明,基于多层选择理论和个体论的两种模型在数学上是等价的。本文的主张是:在还原论和基因决定论的框架内,不可能有独立的群体定义;对群体选择的理解一定要依赖于群体结构的假定。     

“流域”及其相关术语的梳理与厘定

流域是一个在水文学、地貌学等学科中普遍使用的概念，然而在不同学科甚至同一学科中都呈现出术语使用混乱的问题。通过梳理“流域”及其相关术语，弄清楚各术语的具体含义及其对应英文术语；针对现行流域概念所存在的两个关键问题——适用性和落脚点，提出狭义流域、广义流域和地貌学流域的概念区分，并厘定流域及其相关概念术语。     

Agnostic Science. Towards a Philosophy of Data Analysis

In this paper we will offer a few examples to illustrate the orientation of contemporary research in data analysis and we will investigate the corresponding role of mathematics. We argue that the modus operandi of data analysis is implicitly based on the belief that if we have collected enough and sufficiently diverse data, we will be able to answer most relevant questions concerning the phenomenon itself. This is a methodological paradigm strongly related, but not limited to, biology, and we label it the microarray paradigm. In this new framework, mathematics provides powerful techniques and general ideas which generate new computational tools. But it is missing any explicit isomorphism between a mathematical structure and the phenomenon under consideration. This methodology used in data analysis suggests the possibility of forecasting and analyzing without a structured and general understanding. This is the perspective we propose to call agnostic science, and we argue that, rather than diminishing or flattening the role of mathematics in science, the lack of isomorphisms with phenomena liberates mathematics, paradoxically making more likely the practical use of some of its most sophisticated ideas.     

ISO、IEC和ITU-T智慧城市定义分析

智慧城市定义是认识其知识单元和理解其本质特征、构建共识的基础.文章采用ISO 704:2009的理论框架,分析了ISO、IEC和ITU-T对智慧城市的定义,通过解构定义的智慧城市对象、利益相关方、涉及领域、智慧城市实现目标及愿景和实现路径,得出了三大国际标准化组织的智慧城市核心概念、概念关系和其认知视角,通过对三大标准化组织14位专家的问卷调查分析摸清了智慧城市核心概念的不同认知.基于系统方法和综合集成思想提出了多维度构建统一智慧城市定义的建议,为三大标准化组织智慧城市定义的标准化协同和融合提供了有效路径.     

ISO、IEC和ITU-T智慧城市定义分析

智慧城市定义是认识其知识单元和理解其本质特征、构建共识的基础.文章采用ISO 704:2009的理论框架,分析了ISO、IEC和ITU-T对智慧城市的定义,通过解构定义的智慧城市对象、利益相关方、涉及领域、智慧城市实现目标及愿景和实现路径,得出了三大国际标准化组织的智慧城市核心概念、概念关系和其认知视角,通过对三大标准化组织14位专家的问卷调查分析摸清了智慧城市核心概念的不同认知.基于系统方法和综合集成思想提出了多维度构建统一智慧城市定义的建议,为三大标准化组织智慧城市定义的标准化协同和融合提供了有效路径.