Science and the Concept of Evolution: From the Big Bang to the Origin and Evolution of Life

The common thread of evolution runs through all science disciplines, and the concept of evolution enables students to better understand the nature of the universe and our origins. “Science and the Concept of Evolution” is one of two interdisciplinary science Core courses taken by Dowling College undergraduates as part of their General Education requirements. The course examines basic principles and methods of science by following the concept of evolution from the big bang to the origin and evolution of life. Case studies of leading scientists illustrate how their ideas developed and contributed to the evolution of our understanding of the world. Evidences for physical, chemical, and biological evolution are explored, and students learn to view the evolution of matter and of ideas as a natural process of change over space and time.     

Losing Sight of Regressive Evolution

When we teach evolution to our students, we tend to focus on “constructive” evolution, the processes which lead to the development of novel or modified structures. Most biology students are familiar with the subjects of finches’ beaks, giraffes’ necks, and hair in mammals. Of course, there is nothing inherently wrong with a constructivist approach to teaching evolution, but if it is our only focus, we may overlook the flip side of the coin. By the flip side of the coin, of course, we are referring to regressive evolution: the loss or degeneration of a trait. Regressive evolution does not often make its way into biology textbooks, but it is of great relevance nonetheless. In all likelihood, when a new trait evolves or an existing one is modified, something is sacrificed in return. In order to develop a flipper, a marine mammal must sacrifice individual digits. You may be familiar with one or more of the following familiar characters lost through regressive evolution: teeth in birds, scales in mammals, and tails in higher primates. For aficionados of cave biology like us, one of the most interesting examples of regressive evolution concerns cave fish: Why do cave fish lose their eyes?     

Teaching Evolution in Primary Schools: An Example in French Classrooms

Teaching evolution in primary schools is important for spreading evolutionary knowledge and scientific methodology. Through constructing simple interrelationship trees, pupils gain scientific knowledge, scientific methodology, and argumentation skills. Activities conducted in French primary schools are described in this paper.     

Index to Vegetatio,volumes 51–73, and some notes on the position of the journal

An index is presented of 375 articles which appeared in Vol. 51–73 of Vegetatio. A Source index is followed by a Keyword index, a Discipline index, a Vegetation type index, a Geographical index, and a Latin name index for taxa and syntaxa. The codes used for discipline, vegetation type and geographic area are the same as those used in the Index Vol. 1–50. After a short introduction a history of the journal is presented, followed by some statistics on the origin of the authors and the type of article, for seven periods covering the entire history of the journal since 1948. Finally the codes are elucidated.     

Speciation and Bursts of Evolution

A longstanding debate in evolutionary biology concerns whether species diverge gradually through time or by rapid punctuational bursts at the time of speciation. The theory of punctuated equilibrium states that evolutionary change is characterised by short periods of rapid evolution followed by longer periods of stasis in which no change occurs. Despite years of work seeking evidence for punctuational change in the fossil record, the theory remains contentious. Further there is little consensus as to the size of the contribution of punctuational changes to overall evolutionary divergence. Here we review recent developments which show that punctuational evolution is common and widespread in gene sequence data.     

Evolution of virulence in a heterogeneous host population

Abstract.— There is a large body of theoretical studies that investigate factors that affect the evolution of virulence, that is parasite-induced host mortality. In these studies the host population is assumed to be genetically homogeneous. However, many parasites have a broad range of host types they infect, and trade-offs between the parasite virulence in different host types may exist. The aim of this paper is to study the effect of host heterogeneity on the evolution of parasite virulence. By analyzing a simple model that describes the replication of different parasite strains in a population of two different host types, we determine the optimal level of virulence in both host types and find the conditions under which strains that specialize in one host type dominate the parasite population. Furthermore, we show that intrahost evolution of the parasite during an infection may lead to stable polymorphisms and could introduce evolutionary branching in the parasite population.     

植物着丝粒结构及进化的研究进展

植物着丝粒是染色体重要结构域,介导动粒装配。不同物种间着丝粒重复序列快速趋异进化,着丝粒功能保守,确保有丝分裂和减数分裂过程中染色体正确分离和准确传递。伴随染色质免疫共沉淀技术(Chromatin immunoprecipitation, ChIP)、ChIP 与高密度芯片相结合技术(ChIP-chip)、ChIP 与高通量测序相结合技术(ChIP-seq)的应用,植物着丝粒研究获得里程碑式进展:某些模式植物着丝粒DNA 序列、蛋白质结构、功能获得大量新认识;着丝粒基本蛋白质组蛋白H3 被用来界定着丝粒大小和边界;某些非着丝粒区域被激活为新着丝粒,在世代传递中保持稳定性。本文对植物着丝粒结构、功能、进化研究进行了综述,并探讨了植物着丝粒研究存在的问题。     

Evolution of glycoproteins as judged by the frequency of occurrence of the tripeptides Asn-X-Ser and Asn-X-Thr in proteins

Summary A statistical analysis of the data tabulated in the Atlas of Protein Sequence and Structure 1972 indicates that the observed frequency of occurrence of the tripeptides Asn-X-Ser and Asn-X-Thr is approximately one third of the expected in eukaryotic proteins, but in prokaryotic proteins the observation agrees closely with expectation. Thus the lowered frequency of these tripeptides found by Hunt and Dayhoff is restricted to eukaryotic proteins. Of all the Asn-X-Ser/Thr sequences examined, those which contain covalently attached carbohydrates are found only in the extracellular proteins of eukaryote. These observations are discussed in relation to the evolution of glycoproteins which seems to have occurred in the ancestor of eukaryotes after the divergence from prokaryotes.     

A No-Holds-Barred Evolution Curriculum for Elementary and Junior High School Students

Understanding the basic mechanism of evolution by natural selection together with examples of how it works in nature is crucial for explaining and teaching the workings of biology and ecology to young students. Dobzhansky said it best in his advice to educators of biology: “Nothing in biology makes sense except in the light of evolution.” This premise is true at all levels of biology but especially so in the elementary years where foundations of science knowledge are laid. Elementary students are capable of learning cohesive and connected stories of biological principles and learning them within a no-holds-barred arena wherein concepts and processes usually reserved for high school years are taught with special care, appropriate exercises, and patient explanations. This story must include solid introductions to the fundamental principles of evolution by natural selection that are threaded within and alongside those of basic biology and ecology. This paper attempts to make the case for the inclusion of connected stories of biology in the earliest years of education and to include within that education the unifying theme of all biology and ecology studies—evolution.     

Evolution of virulence driven by predator-prey interaction: Possible consequences for population dynamics

The evolution of pathogen virulence in natural populations has conventionally been considered as a result of selection caused by the interactions of the host with its pathogen(s). The host population, however, is generally embedded in complex trophic interactions with other populations in the community, in particular, intensive predation on the infected host can increase its mortality, and this can affect the course of virulence evolution. Reciprocally, in the long run, the evolution of virulence within an infected host can affect the patterns of population dynamics of a predator consuming the host (e.g. resulting in large amplitude oscillations, causing a severe drop in the population size, etc.). Surprisingly, neither the effect of predation on the evolution of virulence within a host, nor the influence of the evolution of virulence upon the consumer's dynamics has been addressed in the literature yet. In this paper, we consider a classical S-I ecoepidemiological model in which the infected host is consumed by a predator. We are particularly interested in the evolutionarily stable virulence of the pathogen in the model and its dependence upon ecologically relevant parameters. We show that predation can prominently shift the evolutionarily stable virulence towards more severe strains as compared to the same system without predation. We demonstrate that the evolution of virulence can result in a succession of dynamical regimes and can even lead to the extinction of the predator in the long run. The presence of a predator can indirectly affect the evolution within its prey since the evolutionarily stable virulence becomes a function of the prey growth rate, which would not be the case in a predator-free system. We find that the evolutionarily stable virulence largely depends on the carrying capacity K of the prey in a non-monotonous way. The model also predicts that in an eutrophic environment the shift of virulence towards evolutionarily stable benign strains can cause demographically stochastic evolutionary suicide, resulting in the extinction of both species, thus artificially maintaining severe strains of pathogen can enhance the persistence of both species.     

Introduction—development and phylogeny of the arthropods: Darwin’s legacy

In the present essay, I first recall the genealogical concept of classification settled by Charles Darwin in the Origin of Species. Darwin tightly linked what we now call phylogeny and development. He often insisted to take into account embryonic and larval characters, most often using as examples his favourite animals, the cirripedes. Then I discuss remaining problems, and also perspectives, to address the link between phylogeny and development in the modern terms of molecular and cladistic phylogenetics and of molecular and genetic developmental biology.     

Evolution of robust and efficient system topologies

Mutation/selection algorithms were applied to increase the efficiency and the robustness of sparse random networks. Selection for better efficiency leads to the well-known star topology, while selection for robustness only results in a relatively dense core and a small periphery. Concomitant selection for both efficiency and robustness leads to networks with intermittent center/periphery values. Networks evolving under multiple attack regimes develop distinct topologies with larger cores, and are characterized by parameter distributions different from those developing under single-attack regimes.     

Misconceptions About the Evolution of Complexity

Despite data and theory from comparative anatomy, embryology, molecular biology, genomics, and evolutionary developmental biology, antievolutionists continue to present the eye as an example of a structure too complex to have evolved. They stress what we have yet to explain about the development and evolution of eyes and present incomplete information as evidence that evolution is a “theory in crisis.” An examination of the evidence, however, particularly evidence that has accumulated in the twentieth and twenty-first centuries, refutes antievolutionists’ claims. The distribution of eyes in extant organisms, combined with what we now know about the control of eye development across diverse groups of organisms, provides significant evidence for the evolution of all major components of the eye, from molecular to morphological, and provides an excellent test of predictions based on common ancestry.     

Evolution of DNA on Y-chromosome in hominoid primates as examined by PCR

Every species of non-human primates, especially those of hominoids, has a variety of reproductive structures and accompanying male traits, such as sexual dimorphism and relative size of testis to body weight, which may be at least partly triggered by DNA on the Y-chromosome. Recently, a panel of PCR (Polymerase Chain Reaction) primer sets were designed to amplify various DNA segments spread over the human Y-chromosome. We applied these primer sets for amplification of DNA segments on the Y-chromosome of hominoid species: chimpanzee, bonobo (Pygmy chimpanzee), gorilla, orangutan, whitehanded gibbon, agile gibbon, and Japanese monkey as an out group. The DNA segments including SRY, testis determining factor, and ZFX/ZFY could be amplified clearly in males of all species examined. These highly conserved genes may serve important biological functions. However, as the phylogenic distance from humans increased, some of the DNA segments could not be amplified. For example, DYZ1 (SY160) could be amplified only using human DNA as a template, and DYF60S1 (SY61), DYZ217 (SY126) and DYS233 (SY148) could be amplified only using human and African great ape DNA. It is interesting to note that locus DYS250 (SY17) could not be amplified in chimpanzee and bonobo but amplified in gorilla and orangutan. Locus DYS251 (SY18) was amplified in all species except the white-handed gibbon. These results indicate that a variety of evolutionary events including mutation, deletion, insertion, and rearrangement occurred in Y-chromosome DNA during primate evolution.     

代谢途径的进化

生物的新陈代谢是通过一系列的代谢途径来实现的.这些调节精妙、相瓦协作的代谢途径是如何进化形成的一直是一个引人入胜的重要问题.自1945年有关该问题的第一个假说--"逆向进化假说"提出以来,迄今已发展出七种假说,包括"逆向进化假说"、"半酶理论"、"向前发展模型"、"酶的招募假说"、"多功能酶特化假说"、"整个代谢途径的复制假说"和"从头创造假说".其中最受关注的是"逆向进化假说"和"酶的招募假说",而最近提出的"多功能酶特化假说"由于有较好的理论基础和实验证据支持,也逐渐引起人们的关注.本文对这些假说逐一作了概述,并结合作者的相关研究工作,对该领域的研究现状和发展趋势进行了分析讨论和展望.     

Self-inflicted Fear of Evolution

Commonly calculated zero probabilities for synthesis of a given protein sequence by chance are that small because the sizes of the proteins taken for the calculations are too large (over 100 residues). Same estimate for 20 - 30 residue chains makes the chance close to 1. Presented at: National Workshop on Astrobiology: Search for Life in the Solar System, Capri, Italy, 26 to 28 October, 2005.     

Using Avida-ED for Teaching and Learning About Evolution in Undergraduate Introductory Biology Courses

Evolution is a complex subject that requires knowledge of basic biological concepts and the ability to connect them across multiple scales of time, space, and biological organization. Avida-ED is a digital evolution educational software environment designed for teaching and learning about evolution and the nature of science in undergraduate biology courses. This study describes our backward design approach to developing an instructional activity using Avida-ED for teaching and learning about evolution in a large-enrollment introductory biology course. Using multiple assessment instruments, we measured student knowledge and understanding of key principles of natural selection before and after instruction on evolution (including the Avida-ED activity). Assessment analysis revealed significant post-instruction learning gains, although certain evolutionary principles (most notably those including genetics concepts, such as the genetic origin of variation) remained particularly difficult for students, even after instruction. Students, however, demonstrated a good grasp of the genetic component of the evolutionary process in the context of a problem on Avida-ED. We propose that: (a) deep understanding of evolution requires complex systems thinking skills, such as connecting concepts across multiple levels of biological organization, and (b) well designed use of Avida-ED holds the potential to help learners build a meaningful and transferable understanding of the evolutionary process. An erratum to this article can be found at     

Solar-Driven Hydrogen Evolution from Value-Added Waste Treatment

Hydrogen is one of the most important energy alternatives to conventional fossil-based fuel. Solar energy based photocatalytic hydrogen evolution (PHE) is a salient approach to produce hydrogen fuel but its efficiency is generally limited by the sluggish and energy-unfavorable oxidation reaction. Meanwhile, waste treatment has become a worldwide problem and clean treatment is highly demanded to avoid the vast greenhouse emission currently. Inspiringly, PHE can be effectively coupled with the favorable photooxidation of many wastes, which kills two birds with one stone. In this review, the recent progress in PHE coupled with waste treatment is presented, where typical solid, liquid, and gas wastes have been briefly discussed. Focusing on the understanding of complicated reaction mechanism and the revelation of oxidation products, the cutting-edge techniques for photophysics and surface chemistry characterization have been analyzed, which are imperative to facilitate the following investigation. Finally, the developing trend and existing issues in current research are also discussed in detail so that a holistic blueprint of PHE coupled with waste treatment can be portrayed to accelerate their application in a realistic world.