Don’t Call it “Darwinism”

Evolutionary biology owes much to Charles Darwin, whose discussions of common descent and natural selection provide the foundations of the discipline. But evolutionary biology has expanded well beyond its foundations to encompass many theories and concepts unknown in the 19th century. The term “Darwinism” is, therefore, ambiguous and misleading. Compounding the problem of “Darwinism” is the hijacking of the term by creationists to portray evolution as a dangerous ideology—an “ism”—that has no place in the science classroom. When scientists and teachers use “Darwinism” as synonymous with evolutionary biology, it reinforces such a misleading portrayal and hinders efforts to present the scientific standing of evolution accurately. Accordingly, the term “Darwinism” should be abandoned as a synonym for evolutionary biology.     

邮票图说达尔文和他的昆虫情缘

今年是伟大的进化论创建者达尔文诞生200周年,本文通过邮票介绍达尔文的昆虫情缘。其中主要内容有:(1)有关纪念达尔文的邮票;(2)他青少年时代是个甲虫迷;(3)在南美和昆虫打交道;(4)昆虫成为进化论的重要元素;(5)他睿智预测马达加斯加存在长喙天蛾,足以为花冠长300mm的兰花授粉。     

车前属(Plantago L.)植物生态与进化生物学研究进展

车前属植物是理论生态学、生理生态学、进化生物学研究的理想材料。本文综述了近年来国内外学者在车前属生态学、进化生物学、系统分类学方面的研究概况。     

Proposal for Teaching Evolutionary Biology: A bridge between research and educational practice

We present quantitative results for the doctoral thesis of the first-named author of this article. The objective was to recommend and test a teaching proposal for core knowledge of evolutionary biology in secondary education. The focus of the study is ‘Problem cores in teaching’. The ‘Weaving evolutionary thinking’ teaching unit, designed for and tested in this study, entailed: selecting basic evolutionary knowledge from the model of evolution through variation and natural selection; designing a coordinated set of activities, teaching resources and evaluation tools; leading a process of teacher training; and building bridges between: the teaching model, research into the teaching of evolutionary biology, our own teaching experience and that of the secondary school teacher who participated in the project. The data collected through questionnaires show significant differences in favour of the experimental group, which means that the proposal may be favourably assessed in the context of Mexican education, in terms of feasibility, relevance and the pedagogical transformation of knowledge.     

Experimenting with Transmutation: Darwin, the Beagle, and Evolution

Detailed analysis of Darwin’s scientific notes and other writings from the Beagle voyage reveals a focus on endemism and replacement of allied taxa in time and in space that began early in the journey. Though it is impossible to determine exactly when Darwin became a transmutationist, the evidence suggests that he was conversant with the transmutational ideas of Lamarck and others and testing (“experimenting” with) them—before he received a copy of Lyell’s Principles of Geology, vol. 2, in November 1832, in which Lyell describes and disputes Lamarck’s theory. To the two rhea species of Patagonia and the four mockingbird species of the Galapagos, we can now add the living Patagonian cavy (rodent) species, and its extinct putatively related species that Darwin collected at Monte Hermoso (Bahia Blanca) in the Fall of 1832, as a replacement pattern absolutely critical to the development of Darwin’s transmutational thinking. Darwin developed his first transmutational theory by adopting “Brocchi’s analogy” (Rudwick 2008)—i.e. that births and deaths of species are analogous to the births and deaths of individuals. Births and deaths of species, as of individuals, are thus explicable in terms of natural causes. Darwin explored these themes and the replacement of the extinct cavy by the modern species explicitly in his February 1835 essay (Darwin 1835a).

动物线粒体假基因的识别及其在进化生物学中的应用

在真菌、昆虫、无脊椎动物和脊椎动物等许多分类单元中,都已发现mtDNA序列的核转座现象。在PCR扩增时,往往同时扩增出mtDNA和细胞核中线粒体假基因(Numts),Numts混淆系统发育和群体遗传研究,得出错误的结果。本文综述了Numts的检查和避免的方法,以及在进化生物学研究中的应用进展。     

Molecular Biology Meets the Learning Sciences: Visualizations in Education and Outreach

Scientific visualizations (illustrations, three-dimensional models, animations, simulations, etc.) play an essential role in biology education, particularly when it comes to communicating phenomena occurring at the submicroscopic levels, beyond the level of unaided observation and without comparable counterparts at the macroscopic level. Students struggle with understanding the sizes of cells, molecules, and atoms in relation to one another as well as differentiating between the various time scales within which each of these levels is functioning. Visualizations can be powerful tools of intuition, playing a critical role in transforming the way students think about the scientific realm. However, a greater understanding of how the design features and affordances of different visualization modalities support learning is required if we are to provide pedagogically impactful experiences.     

Darwin, historical biogeography, and the importance of overcoming binary opposites

It is well known that Darwin and Wallace came to discover the phenomenon of evolution through a historical approach to the geographical distribution of organisms. Before Darwin, evolution was a mere speculation that could be invoked to explain some facts. Darwin's biogeographical argument for evolution is based largely on three main explanatory hypotheses. The first is that the geographical distribution of organisms is historically informative. The second hypothesis is that long-distance dispersal over barriers is one main force (extinction is the other) that modifies the distribution of organisms. The third of Darwin's biogeographical hypotheses is that the factors that shape the distribution of organisms are mainly historical (large, often global and long temporal scales) rather than ecological (small spatial and short temporal scales). From the time of Darwin until now, a wide spectrum of biogeographical schools have provided new insights that challenge the central role of space, dispersal and history as the main explanatory hypotheses for the distribution of organisms, generating three binary opposites: (1) the spatial dimension of evolution: geographical distribution of organisms as historically informative vs. historically uninformative; (2) the processes that modify the geographical distribution of organisms: dispersal vs. vicariance; and (3) the explanation of geographical distribution: history vs. ecology. We analyse these three binary opposites to show that the components of each are complementary rather than antagonistic approaches to the study of biogeography.     

Darwin, Herschel, and the role of analogy in Darwin’s origin

In what follows, I consider the role of analogy in the first edition of Darwin’s Origin. I argue that Darwin follows Herschel’s methodology and hence exploits an analogy between artificial and natural selection that allows him generalize selection as a cause of evolutionary change. This argument strategy is not equivalent to an argument from analogy. Reading Darwin’s argument as conforming to Herschel’s two-step methodology of causal analysis followed by generalization allows us to understand the role and placement of Darwin’s discussion of artificial selection in the Origin, without making the mistake of portraying Darwin’s argument for the existence and character of natural selection as an analogical argument.     

Pharmacology,Genomics, and the Evolutionary Biology of Ageing

Aging is a multifold process affected by many genes and thus many biochemical pathways. This conclusion is underscored by the failure to find simple central controls for the aging process during the 20th Century. This situation poses a fundamental challenge to anti-aging medicine: how to develop effective therapies for a genomically complex pathology. We propose such a strategy. As a first step, we recommend the use of model systems in which significant genetic intervention is not proscribed or impractical. Second, we propose that work with such model systems begin with selected lines that have genetic enhancements that allow increased lifespan. Third, genomic methods should be used to identify a number of biochemical pathways for increasing lifespan. Fourth, biochemical pathways that have been identified in model systems would then be available for pharmaceutical development, first in rodents, eventually in a clinical human population. This may seem to be a cumbersome R&D strategy, but starting with human populations or inadequately pre-screened compounds would be unlikely to succeed because of the complexity of the aging problem.     

Evolutionary Morphology, Innovation, and the Synthesis of Evolutionary and Developmental Biology

One foundational question in contemporarybiology is how to `rejoin evolution anddevelopment. The emerging research program(evolutionary developmental biology or`evo-devo) requires a meshing of disciplines,concepts, and explanations that have beendeveloped largely in independence over the pastcentury. In the attempt to comprehend thepresent separation between evolution anddevelopment much attention has been paid to thesplit between genetics and embryology in theearly part of the 20th century with itscodification in the exclusion of embryologyfrom the Modern Synthesis. This encourages acharacterization of evolutionary developmentalbiology as the marriage of evolutionary theoryand embryology via developmental genetics. Butthere remains a largely untold story about thesignificance of morphology and comparativeanatomy (also minimized in the ModernSynthesis). Functional and evolutionarymorphology are critical for understanding thedevelopment of a concept central toevolutionary developmental biology,evolutionary innovation. Highlighting thediscipline of morphology and the concepts ofinnovation and novelty provides an alternativeway of conceptualizing the `evo and the `devoto be synthesized.     

芸薹属自交不亲和基因的分子生物学及进化模式

芸薹属的自交不亲和性是受单基因座、复等位基因控制的孢子体控制型。自交不亲和基因座位(S-locus)是由多个基因组成的复杂区域,称之为S多基因家族,其大多数成员分布于芸薹属的整个染色体组。目前已鉴定出100多个S等位基因,它们的起源分化始于一千万年前。S-座位上存在的多基因有3种：SRK,SLG和SCR／SPII;SRK和SLG在柱头中表达,SCR／SPII在雄蕊中表达。SRK蛋白在识别同类花粉的过程中起主要作用,而SLG蛋白增强了这种自交不亲和反应。SLG与SRK基因中编码S-结构域的核苷酸序列相似性程度高达85％～98％。基因转换可能是SLG和SRK的高度同源性能够得以保持的原因。SRK,SLG和SCR基因紧密相连,并表现出高水平的序列多样性。SRK与SLG基因间的距离很近,在20～25kb之间。在柱头和花粉中,自交不亲和等位基因之间的共显性关系要比显性和隐性关系更加普遍,这是芸薹属自交不亲和性的一大特点。自交不亲和基因的进化模式存在两种假说：双基因进化模式和中性变异体进化模式;可能存在几种不同的进化方式,它们共同在自然群体中新的S等位基因进化过程中起作用。     

Charles Darwin goes to school: the role of cartoons and narrative in setting science in an historical context

Science education is under revision. Recent changes in society require changes in education to respond to new demands. Scientific literacy can be considered a new goal of science education and the epistemological gap between natural sciences and literacy disciplines must be overcome. The history of science is a possible bridge to link these ‘two cultures’ and to foster an interdisciplinary approach in the classroom. This paper acknowledges Darwin's legacy and proposes the use of cartoons and narrative expositions to put this interesting chapter of science into its historical context. A five-lesson didactic sequence was developed to tell part of the story of Darwin's expedition through South America for students from 10 to 12 years of age. Beyond geological and biological perspectives, the inclusion of historical, social and geographical facts demonstrated the beauty and complexity of the findings that Darwin employed to propose the theory of evolution.     

Evolving cell models for systems and synthetic biology

This paper proposes a new methodology for the automated design of cell models for systems and synthetic biology. Our modelling framework is based on P systems, a discrete, stochastic and modular formal modelling language. The automated design of biological models comprising the optimization of the model structure and its stochastic kinetic constants is performed using an evolutionary algorithm. The evolutionary algorithm evolves model structures by combining different modules taken from a predefined module library and then it fine-tunes the associated stochastic kinetic constants. We investigate four alternative objective functions for the fitness calculation within the evolutionary algorithm: (1) equally weighted sum method, (2) normalization method, (3) randomly weighted sum method, and (4) equally weighted product method. The effectiveness of the methodology is tested on four case studies of increasing complexity including negative and positive autoregulation as well as two gene networks implementing a pulse generator and a bandwidth detector. We provide a systematic analysis of the evolutionary algorithm’s results as well as of the resulting evolved cell models.     

An outline for data analysis in phytosociology: past and present

As vegetation science develops its formalized methodology increased in importance. At the beginning of the century traditional European schools of phytosociology applied an intuitive classification and ordering scheme to establish vegetation units. The introduction of computer-supported data analysis into vegetation science accelerated the formalization. The present paper presents a formal outline for phytosociology and community analysis. In this scheme we distinguish different data states which are connected by active data handling. Data sampling and subsequent analysis can be understood as filtering processes, making theoretical assumptions in vegetation science very important. The model implied provides a basis for discussing potential problems and possibilities in vegetation science.Abbreviations PCA = Principal Component Analysis     

Automata, Living and Non-Living: Descartes' Mechanical Biology and His Criteria for Life

Despite holding to the essential distinction between mind and body, Descartes did not adopt a life-body dualism. Though humans are the only creatures which can reason, as they are the only creatures whose body is in an intimate union with a soul, they are not the only finite beings who are alive. In the present note, I attempt to determine Descartes' criteria for something to be 'living.' Though certain passages associate such a principle with the presence of a properly functioning heart, I show that there are important reasons for also understanding life in terms of a degree of complexity of design.     

中国植物发育生物学若干重要领域的研究回顾

植物发育是指从种子萌发经过营养生长、开花与花器官发育、受精结果形成新一代的有序过程。每一个时期具有复杂的代谢和基因表达与调控网络。过去的数 10年中我国在该领域的研究取得了许多重要的进展 ,特别是近 10年来发育生物学已经从以往的以描述为主要特征发展到在分子水平上阐明发育控制的机理。花器官的发育研究是发育生物学研究最具突破性的领域 ,开花和营养器官的发育已经成为新的研究热点。本文按照植物发育的时间顺序 ,回顾了我国发育生物学若干重要领域的重要研究进展 ,并展望了基因组时代给发育生物学研究带来的新的机遇和研究平台     

中国植物发育生物学若干重要领域的研究回顾

植物发育是指从种子萌发经过营养生长、开花与花器官发育、受精结果形成新一代的有序过程.每一个时期具有复杂的代谢和基因表达与调控网络.过去的数10年中我国在该领域的研究取得了许多重要的进展,特别是近10年来发育生物学已经从以往的以描述为主要特征发展到在分子水平上阐明发育控制的机理.花器官的发育研究是发育生物学研究最具突破性的领域,开花和营养器官的发育已经成为新的研究热点.本文按照植物发育的时间顺序,回顾了我国发育生物学若干重要领域的重要研究进展,并展望了基因组时代给发育生物学研究带来的新的机遇和研究平台.