The rebirth of rational morphology

This paper examines a new challenge to neo-Darwinism, a movement known as process structuralism. The process structuralist critique of neo-Darwinism holds 1) that there are general laws in biology and that biologists should search for these laws; 2) that there are general forms of morphology and development and that biologists should attempt to uncover these forms; 3) that organisms are unified wholes that cannot be understood without adopting a holistic perspective; and 4) that no special, causal primacy should be given to the genes in development and morphology. This paper places process structuralism in its historical context, examines the philosophical underpinnings of the movement, and discusses some of the evidence used to support its claims.     

Physics met biology, and the consequence was..

We summarise the contributions to the discussion and the links between them. The complex relationship between the physical and biological sciences demonstrates three "axes of tension": the role of simulation, the interplay between levels of explanation, and the generality of "laws". We identify examples of true synergy between approaches that genuinely explore new research territory, and underscore the contemporary value of the type of discussions contained in this volume.     

Axiomatization of genetics. 1. Biological meaning

Axiomatization is a trend in science to settle and reduce fundamental assertions, from which all the others are deducible. Classical genetics has been extensively axiomatized and formalized by Woodger (1952), who resorted to 53 axioms and 12 theorems. The molecular settlement of modern genetics provides the basis for a different axiomatic theory. In this paper 3 axioms and 14 theorems are informally expressed. They cover a few elementary laws of "chromosome genetics" in Eukaryotes. The biological problems connected with the further development of this first attempt are discussed.     

Statistical limitations on molecular evolution

Complexity of functions evolving in an evolution process are expected to be limited by the time length of an evolution process among other factors. This paper outlines a general method of deriving function-complexity limitations based on mathematical statistics and independent from details of a biological or genetic mechanism of the evolution of the function. Limitations on the emergence of life are derived, these limitations indicate a possibility of a very fast evolution and are consistent with "RNA world" hypothesis. The discussed method is general and can be used to characterize evolution of more specific biological organism functions and relate functions to genetic structures. The derived general limitations indicate that a co-evolution of multiple functions and species could be a slow process, whereas an evolution of a specific function might proceed very fast, so that no trace of intermediate forms (species) is preserved in fossil records of phenotype or DNA structure; this is consistent with a picture of "punctuated equilibrium".     

Thoughts on the cultural evolution of man. Developmental imprinting and transgenerational effect

The biological evolution of man stopped since it has been conveyed to the objects, created by man. This paper introduces the concept of "conveyed evolution". Being part of the cultural evolution, the conveyed evolution is a continuation of the biological one. There are several similarities between the laws of biological and conveyed evolution, albeit the differences are important as well. Some laws of the conveyed evolution are described here. The conveyed evolution has man-made repair mechanisms (medicine, protection of environment) which defend man from harm. Man's fragility limits the progress of conveyed evolution. However, artificial compounds or environmental pollutants which are provoked by the conveyed evolution induce chemical (hormonal) imprinting in the developmental critical periods, which is transmitted to the progeny generations (transgenerational effect). This could cause evolutionary alterations without mutation.     

Minimal mixture principle as a method of choosing the form of a dynamic model]

The extremality principle for molecular processes in biological systems is considered. The principle is based on an assumption that the main function of biological processes is the separation of the "product" from the "scheme". The form of the dynamical model of the process is determined from the requirement of the "minimum mixture". As an example Selkov's model of glycolysis is considered.     

合成生物学及其在生物技术中的应用进展

合成生物学是一门21世纪生物学的新兴学科,它着眼生物科学与工程科学的结合,把生物系统当作工程系统"从下往上"进行处理,由"单元"(unit)到"部件"(device)再到"系统"(system)来设计,修改和组装细胞构件及生物系统.合成生物学是分子和细胞生物学、进化系统学、生物化学、信息学、数学、计算机和工程等多学科交叉的产物.目前研究应用包括两个主要方面:一是通过对现有的、天然存在的生物系统进行重新设计和改造,修改已存在的生物系统,使该系统增添新的功能.二是通过设计和构建新的生物零件、组件和系统,创造自然界中尚不存在的人工生命系统.合成生物学作为一门建立在基因组方法之上的学科,主要强调对创造人工生命形态的计算生物学与实验生物学的协同整合.必须强调的是,用来构建生命系统新结构、产生新功能所使用的组件单元既可以是基因、核酸等生物组件,也可以是化学的、机械的和物理的元件.本文跟踪合成生物学研究及应用,对其在DNA水平编程、分子修饰、代谢途径、调控网络和工业生物技术等方面的进展进行综述.     

The Ideological Bases of Lévi-Strauss's Structuralism

It is clear that Lévi-Strauss combines in his writings, and often inextricably, the roles of anthropologist (read scientist) and philosopher (read ideologist). This rather unusual combination of anthropological and philosophical dimensions of Lévi-Strauss's thought is the result of two tendencies that often seem to be pulling in different directions: his scientific conception of socio-cultural phenomena (or the delineation of a scientific method for harnessing human behavior under the rubric of sociological laws), on the one hand, and his conception of what society should be (or the ideological statement of what constitutes a "good sociological life"), on the other. In order to understand the nature of structuralism and Lévi-Strauss's contributions to anthropological theory and practice, these two aspects of his thought must be clearly distinguished. This is what I hope to accomplish in this article.     

Concepts of rational taxonomy

The problems are discussed related to development of concepts of rational taxonomy and rational classifications (taxonomic systems) in biology. Rational taxonomy is based on the assumption that the key characteristic of rationality is deductive inference of certain partial judgments about reality under study from other judgments taken as more general and a priory true. Respectively, two forms of rationality are discriminated--ontological and epistemological ones. The former implies inference of classifications properties from general (essential) properties of the reality being investigated. The latter implies inference of the partial rules of judgments about classifications from more general (formal) rules. The following principal concepts of ontologically rational biological taxonomy are considered: "crystallographic" approach, inference of the orderliness of organismal diversity from general laws of Nature, inference of the above orderliness from the orderliness of ontogenetic development programs, based on the concept of natural kind and Cassirer's series theory, based on the systemic concept, based on the idea of periodic systems. Various concepts of ontologically rational taxonomy can be generalized by an idea of the causal taxonomy, according to which any biologically sound classification is founded on a contentwise model of biological diversity that includes explicit indication of general causes responsible for that diversity. It is asserted that each category of general causation and respective background model may serve as a basis for a particular ontologically rational taxonomy as a distinctive research program. Concepts of epistemologically rational taxonomy and classifications (taxonomic systems) can be interpreted in terms of application of certain epistemological criteria of substantiation of scientific status of taxonomy in general and of taxonomic systems in particular. These concepts include: consideration of taxonomy consistency from the standpoint of inductive and hypothetico-deductive argumentation schemes and such fundamental criteria of classifications naturalness as their prognostic capabilities; foundation of a theory of "general taxonomy" as a "general logic", including elements of the axiomatic method. The latter concept constitutes a core of the program of general classiology; it is inconsistent due to absence of anything like "general logic". It is asserted that elaboration of a theory of taxonomy as a biological discipline based on the formal principles of epistemological rationality is not feasible. Instead, it is to be elaborated as ontologically rational one based on biologically sound metatheories about biological diversity causes.     

TRENDS IN AVIAN SYSTEMATICS

The classical "new systematics" with its replacement of the monotypic by the polytypic species, and of the morphological by the biological species concept, is now so universally accepted in ornithology that it can hardly be considered any longer as "new". Present trends indicate two areas of avian systematics favourable for active expansion, population systematics and phylogenetic systematics. Instead of describing the population structure of species in terms of subspecies, the trend will be to describe it in terms of "geographical isolates", "population continuats", and "zones of secondary intergradation" of former geographic isolates. Such an analysis can shed much light on the ecological requirements of species and on their former history. The other area of new avian systematics is a re-activated study of the higher categories of birds, with new methods and interpreted by a re-evaluated set of phylogenetic and evolutionary concepts.     

The significance of modular design in the investigation of processes of system self-organization

A model of the process of determined system self-organization based on system-forming modular water structures is proposed. The arrangement and symmetry of these structures, described by the symmetry groups entanglement, matches the basic principles of system self-organization: "system of systems", "recognition", "all-or-none". Crystallography modular generalization engulfs all stable forms of condensed state, including the bound water structures--matrices for the self-organization of biological systems. The bound water structures, besides being matrices, accomplish the metric selection of other structural components of biological systems capable of self-organization into a whole system by creating numerous directed weak bonds among them.     

组蛋白去乙酰化酶6:异常蛋白降解的关键调控因子

组蛋白去乙酰化酶6(HDAC6)是位于胞浆中的一种去乙酰化酶,参与调控细胞内多种重要的生物活性,可使α-微管蛋白(α-tubulin)、热休克蛋白90(Hsp90)和皮肌动蛋白(cortactin)去乙酰化,并与多种蛋白质缔结形成复合物。在细胞培养中,当产生的错误折叠蛋白超过了分子伴侣再折叠及泛素蛋白酶体系统(UPS)处理能力时,HDAC6可将其特异转运到细胞核周结构——异常蛋白包涵体(aggresome)中,从而使之被自噬有效降解,因此认为HDAC6在异常蛋白降解中发挥了关键的调控功能,是"蛋白构象病"的潜在治疗靶点。     

Darwin's laws

There is widespread agreement among contemporary philosophers of biology and philosophically-minded biologists that Darwin's insights about the intrusion of chance processes into biological regularities undermines the possibility of there being biological laws. Darwin made references to "designed laws." He also freely described some laws as having exceptions. This paper provides a philosophical analysis of the notion of scientific laws that was dominant in Darwin's time, and in all probability the one which he inherited. The analysis of laws is then used to show how it could have been natural for Darwin to believe in designed laws that had exceptions, and to highlight the continuity between the metaphysics of pre-Darwinian, Darwinian, and contemporary biological science. One important result is the removal of one motivation for the anti-laws sentiment in philosophy and biology.     

基于设计的生物大分子成药性优化策略研究进展

目前生物药物正处在高速发展阶段,但生物大分子的一些固有特性限制了其成药性,使得很多具有良好治疗潜能的生物大分子 最终不能开发成药物,因而严重制约了生物药物的发展。生物药物开发的瓶颈已从“新分子的产生”转向“如何获得具有优良生理特性 和预期治疗效果的有效药物”。近年来,通过合理设计改造生物大分子高级结构以优化其成药性的研究获得了快速发展。综述基于设计 的生物大分子成药性优化策略研究进展。     

Translating the message

The "one gene = one protein" model for understanding the genome is well-known. But, as with most biological "rules", it has its exceptions. The viral family that brings polio, the common cold and foot-and-mouth disease translates its entire genome into one long "polyprotein". The study of this translation strategy is bringing to light new targets for fighting disease and new techniques for the biotech industry.     

The Ambiguity of the Word "Complexity" a Proposal for Clarification

There are two different ways of defining complexity.1) Traditionally, the word "complexity" is considered synonymous to "organization". The transformation of species is an expression of victory against random indifferencism.2) The means of measuring complexity that was conceived by Kolmogorov has the advantage of having an external reference. Therefore, its logical reliability is considerable. But Kolmogorov's complexity will be at its best in cases of pure randomness.These mutually incompatible definitions explicitly demand a classification system.The first definition of complexity is contrary to the second one. This must be explained more precisely in order not to disturb the logic of Kolmogorov's conception and to enable to add to this conception, as closely as possible, along the logical rules derived from Gödel's incompleteness.The author proposes a beginning of complexity typology, founded on the necessity of laws that rule a random substract aiming at organization. The generality of laws to be selected will have a direct effect on the logical strength of the "biologists' definition" of complexity.Two fundamental laws are expressed, one derived from mathematics and the other from physics, two fields alien to biology. This fact improves the logical accordance to the argument.     

Bio-steps beyond Turing

Are there 'biologically computing agents' capable to compute Turing uncomputable functions? It is perhaps tempting to dismiss this question with a negative answer. Quite the opposite, for the first time in the literature on molecular computing we contend that the answer is not theoretically negative. Our results will be formulated in the language of membrane computing (P systems). Some mathematical results presented here are interesting in themselves. In contrast with most speed-up methods which are based on non-determinism, our results rest upon some universality results proved for deterministic P systems. These results will be used for building "accelerated P systems". In contrast with the case of Turing machines, acceleration is a part of the hardware (not a quality of the environment) and it is realised either by decreasing the size of "reactors" or by speeding-up the communication channels. Consequently, two acceleration postulates of biological inspiration are introduced; each of them poses specific questions to biology. Finally, in a more speculative part of the paper, we will deal with Turing non-computability activity of the brain and possible forms of (extraterrestrial) intelligence.     

微生物微纳米生物制造的前沿与展望

自然界中微生物种类极为丰富,尺寸涵盖了纳米级与微米级.微生物细胞培养成本低廉,生长繁殖迅速,具有丰富的遗传表现型,因此微生物是可用于纳米、微米以及多层次跨尺度加工的天然“基本单元”和“底盘细胞”.“基于微生物”的生物制造目的是利用微生物的特异结构和多样功能进行仿生和调控,操纵微生物进行加工组装,从而获得新材料、新器件.同时,建立深入研究微生物行为模式的新技术与新方法,为揭示传统方法所未涉及的基本科学问题提供新的平台.以下将分别从纳米和微米两个尺度以及利用微生物的结构或功能两个角度来概述基于微生物的微纳米生物制造的前沿进展.     

孤立湿地研究进展

孤立湿地作为湿地的重要组成部分,在人类社会发展中作用逐渐凸显。对术语"孤立湿地"的定义国外进行较早,美国官方将孤立湿地定义为与可流动水体不相邻或不通过地表水相联系的湿地,而我国仅提出了与孤立湿地相关的概念,如"环型湿地"、"碟型洼地"、湿地的"景观破碎化"等。孤立湿地的类型与特征研究相对较少,没有形成完整的理论体系,仅提出孤立性、水文连通性、生物连通性等特征。孤立湿地的功能研究是孤立湿地研究的重点,从孤立湿地的气候、水文和水质、生境等功能进行阐述。对于孤立湿地的保护,国外已有明确的法律和相应的措施,而我国在此方面需要进一步完善。通过对孤立湿地的定义、类型、特征、功能和保护进行了综述,并对未来我国孤立湿地研究的热点和方向进行了初步展望。