恢复启蒙的探究

自然界因果系列从比较一般的现象出发,一步一步地走向那些从它们之中产生出来的逐渐复杂和特殊的现象。这就是在自然科学中一直进化发展的、发挥统一作用和非常富有成效的对世界的理解。人类关于自然界以及人类自身的知识越来越表现出知识统一的趋势。这种同一性根源于包括智力活动在内的一切活动在本质上都是物质的这一事实,这一事实必然导致文化相对主义的破产和自然科学、社会科学以及人文科学的最终整合。

新书架

《毛泽东的军事高参郭化若》常建忠著,上海人民出版社出版。郭化若曾多年与毛泽东的军事生涯相伴,辅佐毛泽东指挥反'围剿'、出奇兵、建红军、抗日反蒋,功勋卓著。本书记述了这位儒将的一生。介绍了他在任红一方面军参谋处长、参谋长、抗大三分校校长、军事学院教育长、军事科学院副院长等要职时的峥嵘岁月,他的杰出智慧、运筹帷幄和出众的才华。

Characterization of defensin gene from abalone Haliotis discus hannai and its deduced protein

Defensin is one of preserved ancient host defensive materials formed in biological evolution. As a regulator and effector molecule, it is very important in animals＇ acquired immune system. This paper reports the defensin gene from the mixed liver and kidney cDNA library of abalone Haliotis discus hannai Ino. Sequence analysis shows that the gene sequence of full-length cDNA encodes 42 mature peptides （including six Cys）, molecular weight of 4 323 Da, and pI of 8.02. Amino acid sequence homology analysis shows that the peptides are highly similar （70% in common） to other insects defensin. Because of a typical insect-defensin structural character of mature peptide in the secondary structure, the polypeptide named Haliotis discus defensin （hd-def）, a novel of antimicrobial peptides, belongs to insects defensin subfamily. The RT-PCR result of Haliotis discus defensin shows that the gene can be expressed only in the hepatopancreas by Gram-negative and positive bacteria stimulation, which is ascribed to inducible expression. Therefore, it is revealed that the Haliotis discus defensin gene expression was related to the antibacterial infection of Haliotis discus hannai Ino.

Biogeography and Evolutionary Factors Determine Genetic Differentiation of Pinus mugo(Turra) in the Tatra Mountains(Central Europe)

Inter Simple Sequence Repeats （ISSR） markers were used to assess genetic diversity within and among populations of dwarf mountain pine （Pinus rnugo Turra） growing in the Tatra National Park （UNESCO Biosphere Reserve） in Southern Poland （Central Europe）. The analyzed population belongs to two different geobotanical sub-districts： the Western and High Tatras. The level of genetic diversity assessed in this study for P. mugo is generally comparable to that reported for the other pine species in the Pinaceae family assessed by ISSR markers, especially with respect to Nei＇s genetic diversity and the percentage of polymorphic bands. Bayesian analysis clustered the analyzed populations into two groups, corresponding to their geobotanical locations in the Tatras. Significant divergence between the two genetical clusters was supported by the results of Analysis of Molecular Variance （AMOVA）. According to the Mantel test, there was no correlation between the genetic distance and the geographical distance. The present study confirms the existence of two genetically distinct dusters of P. mugo populations in the Tatra Mountains. The observed high population-genetic differentiation of P.mugo in the Tatras could be attributed to several genetic, environmental and historical factors occurring in this mountain area.

Hybrid zone and its genetic analysis: implication for conservation

Hybrid zone is a very critical concept within the evolutionary biology, because it would offer us a better insight to understand the evolutionary role of gene flow and hybridization based on the cline model. This minireview presents an expatiation of history perspectives and research developments upon basic concepts including hybrid zones, hybridization, hybrid and its the genetic cline model. Moreover, by figuring out the existing problem around the hybrids within conservative theory and practices, it suggests that the theory of hybrid zone be introduced into conservation biology and it would be provide a broader and more open theoretical background for conservative research and practices.

Global Bioethical Prevention of the Collision of Biological and Cultural Evolution on Miserable Human Survival

With the cultural myth that science can only determine the way the world ＂is＂ （facts）, while humanities, social sciences, lawyers, philosophers, and theologians must determine the way the world ＂ought to be＂ （values）, those in position of global-, national-, and local-political power make major decisions of the use （or non-use） of scientific knowledge and technology. As a result, the human being has created a non-scientifically based cultural environment that is affecting his ability to survive. In effect, cultural evolution is occurring more rapidly than biological evolution that can adapt to the changes brought about in the physical and psycho-social environments. In a pluralistic cultural world, where each society has generated a different view of human nature and different ethical values, the use, misuse, or non-use of scientific and technological advances are derived from these unscientific views of human nature. Since all life depends on limiting interacting environmental and ecological factors, it is imperative that scientific information be used to govern how to minimize irreversible effects on life-sustaining ecological factors, but also scientific information bearing on understanding human nature ought to be integrated into a ＂global bioethics＂. While ethical values cannot be directly derived from scientific factors, it is also true that human values or our ＂ought＂ cannot be maintained in ignorance or defiance of the facts or the ＂is＂.

Effects of Trawl Selectivity and Genetic Parameters on Fish Body Length Under Long-Term Trawling

Long-term fishing pressure affects the biological characteristics of exploited fish stocks. The biological characteristics of hairtail(Trichiurus lepturus) in the East China Sea are unable to recover because of long-term trawling. Fishing induces evolutionary effects on the fish's biological characteristics. Evidence of these changes includes small size at age, a shift to earlier age structure, and early maturation. Natural and artificial selection usually affect the fish's life history. Selection can induce different chances of reproduction, and individual fish can give a different genetic contribution to the next generation. In this study, analysis of time-dependent probability of significance and test of sensitivity were used to explore the effects of fish exploitation rate, mesh size, and heritability with long-term trawling. Results showed that fishing parameters were important drivers to exploited fish population. However, genetic traits altered by fishing were slow, and the changes in biological characteristics were weaker than those caused by fishing selection. Exploitation rate and mesh size exhibited similar evolutionary trend tendency under long-term fishing. The time-dependent probability of significance trend showed a gradual growth and tended to be stable. Therefore, the direction of fishing-induced evolution and successful management of fish species require considerable attention to contribute to sustainable fisheries in China.

Biology and Culture

Human beings do not live in nature, they live in culture. Contrary to biological evolution, which is based on genetic inheritance, cultural change is transmitted by instruction. Simple beginnings of culture have been observed in various animals. However, the much advanced human culture became possible by its transmission by language, and by its being cumulative. The concept of cultural change as a progressive process, popular by 18th and 19th centuries thinkers, is nowadays rejected, and the uniqueness of each culture stressed. Although, there are some similarities between biological evolution and cultural change, important differences between these processes are emphasized. The rapid rate of cultural change （especially its technological aspect）, as compared to the rate of biological evolution, is noted. In addition, some cultural changes led to new phenomena, which in a time of crisis can be annulled. The possible consequences of the different rate of these two processes for humans as individuals, and for their societies are discussed.

Chromosomal Engineering of Escherichia coli for Efficient Production of Coenzyme Q_(10)

The plasmid-expression system is routinely plagued by potential plasmid instability. Chromosomal integration is one powerful approach to overcome the problem. Herein we report a plasmid-free hyper-producer E.coli strain for coenzyme Q10 production. A series of integration expression vectors, pxKC3T5b and pxKT5b, were constructed for chemically inducible chromosomal evolution(multiple copy integration) and replicon-free and markerless chromosomal integration(single copy integration), respectively. A coenzyme Q10 hyper-producer Escherichia coli TBW20134 was constructed by applying chemically inducible chromosomal evolution,replicon-free and markerless chromosomal integration as well as deletion of menaquinone biosynthetic pathway.The engineered E. coli TBW20134 produced 10.7 mg per gram of dry cell mass(DCM) of coenzyme Q10 when supplemented with 0.075 g·L-1of 4-hydroxy benzoic acid; this yield is unprecedented in E. coli and close to that of the commercial producer Agrobacterium tumefaciens. With this strain, the coenzyme Q10 production capacity was very stable after 30 sequential transfers and no antibiotics were required during the fermentation process. The strategy presented may be useful as a general approach for construction of stable production strains synthesizing natural products where various copy numbers for different genes are concerned.

Microbial Community and Urban Water Quality

Urbanization of China is substantial and growing, and water resources are crucial for both economic and social sustainable development. Unfortunately, the frequency and intensity of water contamination events are increasing at an unprecedented rate and often accompanied by increased pollutant loading due to human activities such as irreversible industrialization and urbanization. The impacts of human pollution are most evident and of greatest concern at the microbial level. The research of the Aquatic Ecohealth Group, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, has been focusing mainly on aquatic microorganisms in the urban environment, from drinking water and landscape water to waste water. Its projects fall into three categories: biomonitoring and bioassessment, microbial ecology and diversity, ecotoxicology and environmental microbiology. Its scientif ic topics include the aquatic ecological safety and microbial food web.

A Batesian mimic and its model share color production mechanisms

Batesian mimics are harmless prey species that resemble dangerous ones （models）, and thus receive protection from predators. How such adaptive resemblances evolve is a classical problem in evolutionary biology. Mimicry is typically thought to be difficult to evolve, especially if the model and mimic produce the convergent phenotype through different proximate mecha- nisms. However, mimicry may evolve more readily if mimic and model share similar pathways for producing the convergent phenotype. In such cases, these pathways can be co-opted in ancestral mimic populations to produce high-fidelity mimicry with- out the need for major evolutionary innovations. Here, we show that a Batesian mimic, the scarlet kingsnake Larnpropeltis elap-soides, produces its coloration using the same physiological mechanisms as does its model, the eastern coral snake Micrurus fulvius. Therefore, precise color mimicry may have been able to evolve easily in this system. Generally, we know relatively little about the proximate mechanisms underlying mimicry .

Research advances in animal distant hybridization

Distant hybridization refers to crosses between two different species or higher-ranking taxa that enables interspecific genome transfer and leads to changes in phenotypes and genotypes of the resulting progeny.If progeny derived from distant hybridization are bisexual and fertile,they can form a hybrid lineage through self-mating,with major implications for evolutionary biology,genetics,and breeding.Here,we review and summarize the published literature,and present our results on fish distant hybridization.Relevant problems involving distant hybridization between orders,families,subfamilies,genera,and species of animals are introduced and discussed,with an additional focus on fish distant hybrid lineages,genetic variation,patterns,and applications.Our review serves as a useful reference for evolutionary biology research and animal genetic breeding.

Are we really seeing the big picture？ Some reflections on the current debates in evolutionary biology

After more than one hundred fifty years of the publication of On the Origin of Species by Darwin, scientists are still arguing on the relative importance of mutation and natural selection, on the driving force of organismal evolution, on microevo- lution and macroevolution, etc. Such periodically repeated debates appeared to have introduced more chaos than musings. What happened and why？ Have we really considered our views, opinions and arguments under the big picture of evolution before pos- ing the questions？ Or are we talking past each other？ We do need some reflections. While we believe that the current evolutionary theory is doing fine, perhaps a refinement or re-encapsulation of its knowledge framework can help promote a better understanding of the evolutionary science as a whole and blow offthe mist over the big picture [Current Zoology 61 （1）： 217-220, 2015 ].

A hybrid biogeography-based optimization method for the inverse kinematics problem of an 8-DOF redundant humanoid manipulator

The redundant humanoid manipulator has characteristics of multiple degrees of freedom and complex joint structure, and it is not easy to obtain its inverse kinematics solution. The inverse kinematics problem of a humanoid manipulator can be formulated as an equivalent minimization problem, and thus it can be solved using some numerical optimization methods. Biogeography-based optimization （BBO） is a new biogeography inspired optimization algorithm, and it can be adopted to solve the inverse kinematics problem of a humanoid manipulator. The standard BBO algorithm that uses traditional migration and mutation operators suffers from slow convergence and prematurity. A hybrid biogeography-based optimization （HBBO） algorithm, which is based on BBO and differential evolution （DE）, is presented. In this hybrid algorithm, new habitats in the ecosystem are produced through a hybrid migration operator, that is, the BBO migration strategy and Did/best/I/bin differential strategy, to alleviate slow convergence at the later evolution stage of the algorithm. In addition, a Gaussian mutation operator is adopted to enhance the exploration ability and improve the diversity of the population. Based on these, an 8-DOF （degree of freedom） redundant humanoid manipulator is employed as an example. The end-effector error （position and orientation） and the ＇away limitation level＇ value of the 8-DOF humanoid manipulator constitute the fitness function of HBBO. The proposed HBBO algorithm has been used to solve the inverse kinematics problem of the 8-DOF redundant humanoid manipulator. Numerical simulation results demonstrate the effectiveness of this method.

Evolution and functional analysis of the Pif97 gene of the Pacific oyster Crassostrea gigas

Mollusc shell matrix proteins （SMPs） are important functional components embedded in the shell and play a role in shell formation. A SMP （Pif177） was identified previously from the nacreous layer of the Japanese pearl oyster Pinctadafucata, and its cleavage products （named pfPif97 and pfPif80 proteins） were found to bind to the chitin framework and induce aragonite crystal formation and orient the c axis. In this study, a homologue of pfPif177 was cloned from the mantle of the Pacific oyster Crassostrea gigas, containing the homologue of pfPif97 only and not pfPif80. This finding hints at the large divergence in gene structure between the two species. This homologue （cgPif97） shares characteristics with pfPif97, and suggests that the biological functions of these two proteins may be similar. The expression pattern of cgPif97 in different tissues and development stages in- dicates that it may play an important role in shell formation of the adult oyster. The morphology of the inner shell surface was af- fected by injected siRNA of cgPif97 and the calcite laths of the shell became thinner and narrower when the siRNA dose in- creased, suggesting that the cgPip7 gene plays an important role in calcite shell formation in C. gigas. In conclusion, we found evidence that the Pif177 gene evolved very fast but still retains a similar function among species [Current Zoology 59 （1）： 109-115, 2013].

Phylogeny and evolutionary history of the silkworm

The silkworm,Bombyx mori,played an important role in the old Silk Road that connected ancient Asia and Europe.However,to date,there have been few studies of the origins and domestication of this species using molecular methods.In this study,DNA sequences of mitochondrial and nuclear loci were used to infer the phylogeny and evolutionary history of the domesticated silkworm and its relatives.All of the phylogenetic analyses indicated a close relationship between the domesticated silkworm and the Chinese wild silkworm.Domestication was estimated to have occurred about 4100 years ago(ya),and the radiation of the different geographic strains of B.mori about 2000 ya.The Chinese wild silkworm and the Japanese wild silkworm split about 23600 ya.These estimates are in good agreement with the fossil evidence and historical records.In addition,we show that the domesticated silkworm experienced a population expansion around 1000 ya.The divergence times and the population dynamics of silkworms presented in this study will be useful for studies of lepidopteran phylogenetics,in the genetic analysis of domestic animals,and for understanding the spread of human civilizations.

Inducible competitors and adaptive diversification

Identifying the causes of diversification is central to evolutionary biology. The ecological theory of adaptive diversi- fication holds that the evolution of phenotypic differences between populations and species--and the formation of new spe- cies-stems from divergent natural selection, often arising from competitive interactions. Although increasing evidence suggests that phenotypic plasticity can facilitate this process, it is not generally appreciated that competitively mediated selection often also provides ideal conditions for phenotypic plasticity to evolve in the first place. Here, we discuss how competition plays at least two key roles in adaptive diversification depending on its pattern. First, heterogenous competition initially generates heterogeneity in resource use that favors adaptive plasticity in the form of ＂inducible competitors＂. Second, once such competitively induced plas- ticity evolves, its capacity to rapidly generate phenotypic variation and expose phenotypes to alternate selective regimes allows populations to respond readily to selection favoring diversification, as may occur when competition generates steady diversifying selection that permanently drives the evolutionary divergence of populations that use different resources. Thus, competition plays two important roles in adaptive diversification---one well-known and the other only now emerging--mediated through its effect on the evolution ofphenotypic plasticity

Rapid progress of DNA replication studies in Archaea,the third domain of life

Archaea,the third domain of life,are interesting organisms to study from the aspects of molecular and evolutionary biology.Archaeal cells have a unicellular ultrastructure without a nucleus,resembling bacterial cells,but the proteins involved in genetic information processing pathways,including DNA replication,transcription,and translation,share strong similarities with those of Eukaryota.Therefore,archaea provide useful model systems to understand the more complex mechanisms of genetic information processing in eukaryotic cells.Moreover,the hyperthermophilic archaea provide very stable proteins,which are especially useful for the isolation of replisomal multicomplexes,to analyze their structures and functions.This review focuses on the history,current status,and future directions of archaeal DNA replication studies.