Biosemiotics: a new understanding of life

Biosemiotics is the idea that life is based on semiosis, i.e., on signs and codes. This idea has been strongly suggested by the discovery of the genetic code, but so far it has made little impact in the scientific world and is largely regarded as a philosophy rather than a science. The main reason for this is that modern biology assumes that signs and meanings do not exist at the molecular level, and that the genetic code was not followed by any other organic code for almost four billion years, which implies that it was an utterly isolated exception in the history of life. These ideas have effectively ruled out the existence of semiosis in the organic world, and yet there are experimental facts against all of them. If we look at the evidence of life without the preconditions of the present paradigm, we discover that semiosis is there, in every single cell, and that it has been there since the very beginning. This is what biosemiotics is really about. It is not a philosophy. It is a new scientific paradigm that is rigorously based on experimental facts. Biosemiotics claims that the genetic code (1) is a real code and (2) has been the first of a long series of organic codes that have shaped the history of life on our planet. The reality of the genetic code and the existence of other organic codes imply that life is based on two fundamental processes--copying and coding--and this in turn implies that evolution took place by two distinct mechanisms, i.e., by natural selection (based on copying) and by natural conventions (based on coding). It also implies that the copying of genes works on individual molecules, whereas the coding of proteins operates on collections of molecules, which means that different mechanisms of evolution exist at different levels of organization. This review intends to underline the scientific nature of biosemiotics, and to this purpose, it aims to prove (1) that the cell is a real semiotic system, (2) that the genetic code is a real code, (3) that evolution took place by natural selection and by natural conventions, and (4) that it was natural conventions, i.e., organic codes, that gave origin to the great novelties of macroevolution. Biological semiosis, in other words, is a scientific reality because the codes of life are experimental realities. The time has come, therefore, to acknowledge this fact of life, even if that means abandoning the present theoretical framework in favor of a more general one where biology and semiotics finally come together and become biosemiotics.     

Understanding the North–South knowledge divide and its implications for policy: a quantitative analysis of the generation of scientific knowledge in the environmental sciences

The paper investigates the scientific knowledge divide in the environmental sciences between developed and developing countries and explores the implications and impacts on both science and policymaking. Quantitative data analysis of more than 6400 scientific papers published in 1993–2003 yield evidence for a growing divide in authorship, publication rates, and location of scientific research in nine environmental journals with high impact factor ratings. In addition to this severe imbalance in publication rates between developed and developing countries, we also find a research bias toward certain eco-climatic zones. More than 80% of papers are published in and about temperate and cold eco-climatic zones. Only 13% of the papers in our study are based on research in the dry sub-tropical and tropical zones, although these eco-climatic zones account for more than 52% of the world's land area. Based on these results, we discuss how the limited empirical source and focus of environmental research undermine the claims of universality of environmental science and what consequences this may have on policymaking processes at different levels. Finally, we briefly explore some short- and long-term strategies to address the knowledge divide.     

Wird die Biologie zur Leitwissenschaft des ausgehenden 20. Jahrhunderts?

At the end of the twentieth century biology starts to take the place of physics as a trend-setting science. Complexity and the dynamics of nature per se are not the reason for this. Actually the construction of nature by mankind today is more complex and more dynamic than ever before. The transfer of scientific patterns, describing nature, into the social sciences is, in fact, a retransfer.     

A review on molecular topology: applying graph theory to drug discovery and design

Molecular topology is an application of graph theory and statistics in fields like chemistry, biology, and pharmacology, in which the molecular structure matters. Its scope is the topological characterization of molecules by means of numerical invariants, called topological indices, which are the main ingredients of the molecular topological models. These are statistical models that are instrumental in the discovery of new applications of naturally occurring molecules, as well as in the design of synthetic molecules with specific chemical, biological, or pharmacological properties. In this review, we focus on pharmacology, which is a novel field of application of molecular topology. Besides summarizing some recent developments, we also seek to bring closer this interesting biomedical application of mathematics to an interdisciplinary readership.

The prospect of alien life in exotic forms on other worlds

The nature of life on Earth provides a singular example of carbon-based, water-borne, photosynthesis-driven biology. Within our understanding of chemistry and the physical laws governing the universe, however, lies the possibility that alien life could be based on different chemistries, solvents, and energy sources from the one example provided by Terran biology. In this paper, we review some of these possibilities. Silanes may be used as functional analogs to carbon molecules in environments very different from Earth; solvents other than water may be compatible for life-supporting processes, especially in cold environments, and a variety of energy sources may be utilized, some of which have no Terran analog. We provide a detailed discussion of two possible habitats for alien life which are generally not considered as such: the lower cloud level of the Venusian atmosphere and Titan’s surface environment.     

滇西北高原湖泊剑湖演变过程及其生态环境效应分析

以滇西北高原湖泊剑湖为研究区,1974—2015年间8期遥感影像为数据源,运用遥感和地理信息系统技术,研究剑湖湖泊近40年间的时空演变过程,探析剑湖湖泊的入湖污染物及其生态环境效应变化。结果表明:近40年来剑湖湖泊面积呈现先明显减少再增加后缓慢减少的变化规律,由1974年的504.47 hm~2减至2015年的451.72 hm~2;目前剑湖水体中COD含量较低,符合地表水环境质量Ⅱ类标准;TP含量满足Ⅲ类标准;TN含量仅可满足IV类标准;剑湖入湖的主要污染源是农村生活污染和农业面源污染;随着时间的演变剑湖湖泊TN、TP污染物浓度呈上升趋势,剑湖湖泊生态系统受到极大干扰。     

环境分子科学与环境纳米技术

传统的分子科学和新兴的纳米技术近年来广泛地渗入和覆盖了环境科学与技术,对环境污染现象的微观过程与机理研究注入了新的活力,进一步加深对环境污染从本质上的认识,为环境保护开展更高效的技术工艺开辟了新的途径．论综合评述了环境分子科学与环境纳米技术的发展概况,并对我国该领域的研究提出一些认识和讨论意见．     

The predictability of evolution: glimpses into a post-Darwinian world

The very success of the Darwinian explanation, in not only demonstrating evolution from multiple lines of evidence but also in providing some plausible explanations, paradoxically seems to have served to have stifled explorations into other areas of investigation. The fact of evolution is now almost universally yoked to the assumption that its outcomes are random, trends are little more than drunkard’s walks, and most evolutionary products are masterpieces of improvisation and far from perfect. But is this correct? Let us consider some alternatives. Is there evidence that evolution could in anyway be predictable? Can we identify alternative forms of biological organizations and if so how viable are they? Why are some molecules so extraordinarily versatile, while others can be spoken of as “molecules of choice”? How fortuitous are the major transitions in the history of life? What implications might this have for the Tree of Life? To what extent is evolutionary diversification constrained or facilitated by prior states? Are evolutionary outcomes merely sufficient or alternatively are they highly efficient, even superb? Here I argue that in sharp contradistinction to an orthodox Darwinian view, not only is evolution much more predictable than generally assumed but also investigation of its organizational substrates, including those of sensory systems, which indicates that it is possible to identify a predictability to the process and outcomes of evolution. If correct, the implications may be of some significance, not least in separating the unexceptional Darwinian mechanisms from underlying organizational principles, which may indicate evolutionary inevitabilities.     

Biogenetic amino acid antagonists

The mode of action of amino acid antagonists of biological origin ist surveyed und the enzymatic reactions with which these antibiotics interfere are described, thus also elucidating the various roles of amino acids in cell physiology. Several organisms, including the antibiotic producer, possess molecular devices for conferring resistance to some of these substances. These antibiotics may be of further value as research tools in molecular biology.     

自然资源与环境安全研究进展

跟踪研究自然资源的演化、开发利用过程调控机理一直是中国科学院地理科学与资源研究所(以下简称我所)资源环境研究领域的重要研究任务和研究方向。论文总结了1950年以来我所自然资源与环境安全研究领域取得的成果与进展,在1950—1978年期间,我所自然资源与环境安全研究以大规模的自然资源调查与综合科学考察为主,丰硕的考察成果对中国的资源开发和区域发展提供了重要科学支持,做出了不可磨灭的贡献,而且在系统地积累科学资料和开拓资源科学方面也发挥了积极作用,它为了解我国资源环境、建立资源科学体系奠定了坚实的基础;1978—2000年期间,我所自然资源与环境安全研究转向了区域资源综合科学考察与资源科学研究并重的格局,完成的一系列考察报告为区域发展指明了路径,为全面认识中国自然资源和开展自然资源综合研究奠定了数据基础。2000年以来,我所自然资源与环境安全研究更加注重学科体系建设,促进了资源科学的学科体系建立;更加注重世界资源研究,将自然资源考察地域拓展到全球范围;更加注重机理过程研究,在资源环境承载力、资源流动、资源安全、生态服务功能等领域进行了理论开拓;更加注重资源开发利用技术研究,在环境修复的理论和技术方面取得了一系列成果。展望未来,我所资源与环境领域研究将会继续以国家重大战略需求为导向,以水资源、土地资源、生物资源、能源及矿产资源等关键资源为主要对象,在以下5个方面开展系统深入的研究,推动资源学科的建设与发展:①区域综合科学考察与资源科学综合研究;②水土资源可持续利用及其复杂性;③自然资源流动过程及其生态环境效应;④世界自然资源态势与国家战略性资源安全;⑤环境修复机理与废弃物资源化利用。     

BLM预测水中重金属生物有效性研究进展

生物配体模型( BLM)是利用环境参数来预测重金属生物有效性的模型.它生物受体位点作为生物配体,考虑了影响生物毒性的水化学性质,并把生物有效性的概念引入到水质标准中,在较宽的模拟水质范围内取得较好的预测效果.生物配体模型是多学科共同发展的成果,综合了金属在水环境中的化学、生物学、生理学等以及计算机科学方面的成果,这学科...     

Evolutionary developmental biology: its concepts and history with a focus on Russian and German contributions

Evolutionary theory has been likened to a “universal acid” (Dennett 1995) that eats its way into more and more areas of science. Recently, developmental biology has been infused by evolutionary concepts and perspectives, and a new field of research—evolutionary developmental biology—has been created and is often called EvoDevo for short. However, this is not the first attempt to make a synthesis between these two areas of biology. In contrast, beginning right after the publication of Darwin’s Origin in 1859, Ernst Haeckel formulated his biogenetic law in 1872, famously stating that ontogeny recapitulates phylogeny. Haeckel was in his turn influenced by pre-Darwinian thinkers such as Karl Ernst von Baer, who had noted that earlier developmental stages show similarities not seen in the adults. In this review, written for an audience of non-specialists, we first give an overview of the history of EvoDevo, especially the tradition emanating from Haeckel and other comparative embryologists and morphologists, which has often been neglected in discussions about the history of EvoDevo and evolutionary biology. Here we emphasize contributions from Russian and German scientists to compensate for the Anglo-American bias in the literature. In Germany, the direct influence of Ernst Haeckel was felt particularly in Jena, where he spent his entire career as a professor, and we give an overview of the “Jena school” of evolutionary morphology, with protagonists such as Oscar Hertwig, Ludwig Plate, and Victor Franz, who all developed ideas that we would nowadays think of as belonging to EvoDevo. Franz ideas about “biometabolic modi” are similar to those of a Russian comparative morphologist that visited Jena repeatedly, A. N. Sewertzoff, who made important contributions to what we now call heterochrony research—heterochrony meaning changes in the relative timing of developmental events. His student I. I. Schmalhausen became an important contributor to the synthetic theory of evolution in Russia and is only partly known outside of the Russian-reading world because only one of his many books was translated into English early on. He made many important contributions to evolutionary theory and we point out the important parallels between Schmalhausen’s ideas (stabilizing selection, autonomization) and C. H. Waddington’s (canalization, genetic assimilation). This is one of the many parallels that have contributed to an increased appreciation of the internationality of progress in evolutionary thinking in the first half of the twentieth century. A direct link between German and Russian evolutionary biology is provided by N. V. Timoféeff-Ressovsky, whose work on, e.g., fly genetics in Berlin is a crucial part of the history of evo-devo. To emphasize the international nature of heterochrony research as predecessor to the modern era of EvoDevo, we include Sir G. R. de Beer’s work in the UK. This historical part is followed by a short review of the discovery and importance of homeobox genes and of some of the major concepts that form the core of modern EvoDevo, such as modularity, constraints, and evolutionary novelties. Major trends in contemporary EvoDevo are then outlined, such as increased use of genomics and molecular genetics, computational and bioinformatics approaches, ecological developmental biology (eco-devo), and phylogenetically informed comparative embryology. Based on our survey, we end the review with an outlook on future trends and important issues in EvoDevo.     

Glycogen with short average chain length enhances bacterial durability

Glycogen is conventionally viewed as an energy reserve that can be rapidly mobilized for ATP production in higher organisms. However, several studies have noted that glycogen with short average chain length in some bacteria is degraded very slowly. In addition, slow utilization of glycogen is correlated with bacterial viability, that is, the slower the glycogen breakdown rate, the longer the bacterial survival time in the external environment under starvation conditions. We call that a durable energy storage mechanism (DESM). In this review, evidence from microbiology, biochemistry, and molecular biology will be assembled to support the hypothesis of glycogen as a durable energy storage compound. One method for testing the DESM hypothesis is proposed.     

分子生物学在渔业环境保护中的运用

分子生物学理论和技术在渔业环境保护与监测工作中的应用越来越得到人们的重视：生物体的多种酶已被用作监测水环境污染的指标；金属硫蛋白等生物体解毒体系在监测和防治水体重金属污染方面发挥显著作用；核酸是生物体遗传信息载体，以核酸质量变化监测水环境污染已取得较好的效果。据此就分子生物学在今后渔业环境保护中的运用提出了观点。     

Combinatorics of aliphatic amino acids

This study combines biology and mathematics, showing that a relatively simple question from molecular biology can lead to complicated mathematics. The question is how to calculate the number of theoretically possible aliphatic amino acids as a function of the number of carbon atoms in the side chain. The presented calculation is based on earlier results from theoretical chemistry concerning alkyl compounds. Mathematical properties of this number series are highlighted. We discuss which of the theoretically possible structures really occur in living organisms, such as leucine and isoleucine with a chain length of four. This is done both for a strict definition of aliphatic amino acids only involving carbon and hydrogen atoms in their side chain and for a less strict definition allowing sulphur, nitrogen and oxygen atoms. While the main focus is on proteinogenic amino acids, we also give several examples of non-proteinogenic aliphatic amino acids, playing a role, for instance, in signalling. The results are in agreement with a general phenomenon found in biology: Usually, only a small number of molecules are chosen as building blocks to assemble an inconceivable number of different macromolecules as proteins. Thus, natural biological complexity arises from the multifarious combination of building blocks.     

国家自然科学基金“土地科学和自然资源管理”申请代码领域研究格局、热点透视与发展展望

支持基础研究是国家自然科学基金的职责使命。自然资源管理是地理科学交叉融合创新的重要领域。划分国家自然科学基金土地科学和自然资源管理申请代码领域的研究方向,分析该领域申报与资助格局,透视研究热点,提出发展展望。研究发现：2021年以来土地科学和自然资源管理领域的申报格局以交叉且偏向人文要素研究为主,交叉类研究占55%以上,人文要素为主类研究占30%,自然要素为主类研究占15%;以土地资源为对象研究占73%,以生态资源为对象占14%,以其他自然资源为对象的研究占13%。资助格局中土地资源类项目占主导,在75%以上,其他自然资源资助比例不高且资助率不稳定,在土地资源中,农用地、建设用地与土地系统是主要资助领域。为推动自然资源管理领域的健康持续发展,要创新该领域研究范式,增强基础研究属性,树立交叉融合研究典范,坚持申请代码初衷内涵。     

阻抗复合消声器的动态特性分析

VW - 0 2 2 7-B型空压机的噪声源 ,其空气动力性噪声最强。拟在空压机进气口安装阻抗复合消声器 ,本文针对由最优化设计方法获得的阻抗复合型消声器模型 ,在未对消声器实物加工之前 ,根据消声器的图纸及有关数据进行了有限元动力计算 ,从而初步了解消声器的动态特性。由此可避免消声器制造的盲目性及重复实验 ,为设计优良消声器提供新的有效途径。     

Honeybees learn floral odors while receiving nectar from foragers within the hive

Recent studies showed that nectar odors brought back by honeybee foragers can be learned associatively inside the hive. In the present study, we focused on the learning abilities of bees, which directly interact via trophallaxis with the incoming nectar foragers: the workers that perform nectar-receiving tasks inside the hive. Workers that have received food directly from foragers coming back from a feeder offering either unscented or scented sugar solution [phenylacetaldehyde (PHE) or nonanal diluted] were captured from two observational hives, and their olfactory memories were tested using the proboscis extension response paradigm. Bees that have received scented solution from incoming foragers showed significantly increased response frequencies for the corresponding solution odor in comparison with those that have received unscented solution. No differences in the response frequencies were found between food odors and colonies. The results indicate that first-order receivers learn via trophallaxis the association between the scent and the sugar solution transferred by incoming foragers. The implications of these results should be considered at three levels: the operational cohesion of bees involved in foraging-related tasks, the information propagation inside the hive related to the floral type exploited, and the putative effect of these memories on future preferences for resources.     

除草剂阿特拉津的使用与危害

文章介绍了目前广泛应用的一种除草剂阿特拉津的使用和特性,阿特拉津被认为是安全的除草剂,但大量研究结果表明,其分子结构稳定, 使用后不易降解,在使用过的水体和土壤中均有检出,长期使用后可对水环境、土壤和动物产生一定的危害,尤其是作为一种环境荷尔蒙,已经发现它能够对水生生物的生长繁殖产生影响,可能产生变性反应,是人类潜在的致癌物.通过对其危害的研究和防范管理,可以减少和避免可能对人类、生态环境带来的进一步危害.