Enforcement Is Central to the Evolution of Cooperation
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AP Biology Planner
COURSE PLANNER Please note that not all activities for the course are listed, and many activities will be supplemented with additional activities such as diagram analysis, practice essays, etc. Intro to AP Biology/Scientific Method This course begins with introducing students to the seven science practices, in addition to the Big Ideas that unify the course. Students complete the lab exercises that emphasize the need for controls in experiments as well as to identify and explain potential sources of error as part of the normal scientific process. Reading in Campbell and Reece: Topics: • Intro to AP biology, the test and how to study. ♣ Activity: Theme-teams: Students research and present scientist who represent each Big Idea in AP Biology. ♣ Activity: Analyzing the AP multiple choice questions with diagrams. • Scientific Method: Steps and controlled experiments ♣ Activity: What is Science? Discussion/Poster Creation. ♣ Activity: Lab Safety activity: NIH’s Student Lab Safety Introduction Course. https://www.safetytraining.nih.gov/introcourse/labsafetyIntro.aspx ♣ Activity: Identify risks in procedures and materials (MSDS analysis) ♣ Activity: Guide to good graphing. ♣ Activity: Examining bias in science. ♣ Lab: Student Designed inquiry. The effect of environmental factors on the metabolic rate of yeast. In this student designed inquiry, students investigate environmental factors as they relate to CO2 production or O2 consumption in yeast. Students must select an independent variable and dependent variable, as well as design an experimental procedure based on an existing lab protocol. ECOLOGY The ecology unit introduces the ideas of energy processes and interactions, which are the focus of Big Idea 2 and 4. Ecology introduces students to creating, analyzing, and evaluating mathematical models in biology and prepares students to tackle evolution, the central unit in AP Biology. -
Sensory and Cognitive Adaptations to Social Living in Insect Societies Tom Wenseleersa,1 and Jelle S
COMMENTARY COMMENTARY Sensory and cognitive adaptations to social living in insect societies Tom Wenseleersa,1 and Jelle S. van Zwedena A key question in evolutionary biology is to explain the solitarily or form small annual colonies, depending upon causes and consequences of the so-called “major their environment (9). And one species, Lasioglossum transitions in evolution,” which resulted in the pro- marginatum, is even known to form large perennial euso- gressive evolution of cells, organisms, and animal so- cial colonies of over 400 workers (9). By comparing data cieties (1–3). Several studies, for example, have now from over 30 Halictine bees with contrasting levels of aimed to determine which suite of adaptive changes sociality, Wittwer et al. (7) now show that, as expected, occurred following the evolution of sociality in insects social sweat bee species invest more in sensorial machin- (4). In this context, a long-standing hypothesis is that ery linked to chemical communication, as measured by the evolution of the spectacular sociality seen in in- the density of their antennal sensillae, compared with sects, such as ants, bees, or wasps, should have gone species that secondarily reverted back to a solitary life- hand in hand with the evolution of more complex style. In fact, the same pattern even held for the socially chemical communication systems, to allow them to polymorphic species L. albipes if different populations coordinate their complex social behavior (5). Indeed, with contrasting levels of sociality were compared (Fig. whereas solitary insects are known to use pheromone 1, Inset). This finding suggests that the increased reliance signals mainly in the context of mate attraction and on chemical communication that comes with a social species-recognition, social insects use chemical sig- lifestyle indeed selects for fast, matching adaptations in nals in a wide variety of contexts: to communicate their sensory systems. -
Framing Major Prebiotic Transitions As Stages of Protocell Development: Three Challenges for Origins-Of-Life Research
Framing major prebiotic transitions as stages of protocell development: three challenges for origins-of-life research Ben Shirt-Ediss1, Sara Murillo-Sánchez2,3 and Kepa Ruiz-Mirazo*2,3 Commentary Open Access Address: Beilstein J. Org. Chem. 2017, 13, 1388–1395. 1Interdisciplinary Computing and Complex BioSystems Group, doi:10.3762/bjoc.13.135 University of Newcastle, UK, 2Dept. Logic and Philosophy of Science, University of the Basque Country, Spain and 3Biofisika Institute Received: 16 February 2017 (CSIC, UPV-EHU), Spain Accepted: 27 June 2017 Published: 13 July 2017 Email: Kepa Ruiz-Mirazo* - [email protected] This article is part of the Thematic Series "From prebiotic chemistry to molecular evolution". * Corresponding author Guest Editor: L. Cronin Keywords: functional integration; origins of life; prebiotic evolution; protocells © 2017 Shirt-Ediss et al.; licensee Beilstein-Institut. License and terms: see end of document. Abstract Conceiving the process of biogenesis as the evolutionary development of highly dynamic and integrated protocell populations provides the most appropriate framework to address the difficult problem of how prebiotic chemistry bridged the gap to full-fledged living organisms on the early Earth. In this contribution we briefly discuss the implications of taking dynamic, functionally inte- grated protocell systems (rather than complex reaction networks in bulk solution, sets of artificially evolvable replicating molecules, or even these same replicating molecules encapsulated in passive compartments) -
Plasticity‐Led Evolution: a Survey of Developmental Mechanisms and Empirical Tests
DOI: 10.1111/ede.12309 PERSPECTIVE Plasticity‐led evolution: A survey of developmental mechanisms and empirical tests Nicholas A. Levis | David W. Pfennig Department of Biology, University of North Carolina, Chapel Hill, Abstract North Carolina Recent years have witnessed increased interest in evaluating whether phenotypic plasticity can precede, facilitate, and possibly even bias adaptive Correspondence “ ‐ ” Nicholas A. Levis, Department of Biology, evolution. Despite accumulating evidence for plasticity led evolution (i.e., CB#3280, University of North Carolina, “PLE”), critical gaps remain, such as: how different developmental Chapel Hill, NC 27599. mechanisms influence PLE; whether some types of traits and taxa are Email: [email protected] especially prone to experience PLE; and what studies are needed to drive the field forward. Here, we begin to address these shortcomings by first speculating about how various features of development—modularity, flexible regulation, and exploratory mechanisms—mightimpactand/orbias whether and how PLE unfolds. We then review and categorize the traits and taxa used to investigate PLE. We do so both to identify systems that may be well‐suited for studying developmental mechanisms in a PLE context and to highlight any mismatches between PLE theory and existing empirical tests of this theory. We conclude by providing additional suggestions for future research. Our overarching goal is to stimulate additional work on PLE and thereby evaluate plasticity’s role in evolution. 1 | INTRODUCTION 2011; West‐Eberhard, 2003). Under this view, novel traits start out evolutionarily as environmentally The environment has long been viewed as crucial in induced phenotypic variants. Later, they come under both selecting on phenotypes and in creating those genetic control through selection on developmental phenotypes in the first place (e.g., Baldwin, 1896, processes. -
Gene-Culture Coevolution, Group Selection, and the Evolution of Cooperation
EC_2018_A12 Gene-Culture coevolution, group selection, and the evolution of Cooperation The Evolution of Cooperation How can altruism / cooperation evolve? 1 EC_2018_A12 Levels of Selection "although a high standard of morality gives but a slight or no advantage to each individual man and his children over the other men of the same tribe (...) an advancement in the standard of morality will certainly give an immense advantage to one tribe over another.” (C. Darwin, Descent of Man, 1871) Levels of Selection Individuals (“basic” [Neo]Darwinism) Genes (“Selfish-gene” Sociobiology) Groups? Multilevel selection? Higher-level adaptations? Genetic Group Selection? “Naïve group selectionism”: The probability of survival of individual living things, or of populations, increases with the degree with which they harmoniously adjust themselves to each other and to their environment. This principle is basic to the concept of the balance of nature, orders the subject matter of ecology and evolution, underlies organismic and developmental biology, and is the foundation for all sociology. (Allee et al. 1949) “The good of the species” (Wynne-Edwards) 2 EC_2018_A12 Levels of Selection Migration, genetic drift, etc: Intergroup effects weaker than intragroup, interindividual selection. Intra x intergroup differences X Wilson DS & Wilson EO (2007) Rethinking the theoretical foundation of sociobiology Multi-level selection/ limits in kin selection theory/ “major transitions” Eusociality: Kin Selection X Individual selection + preadaptations. (communal nests) Nowak, Tarnita & Wilson, “The Evolution of Eusociality”, Nature 2010 (X Abbot et al [+100!], Nature 2011) “Major Transitions” in Evolution Maynard Smith & Szathmáry 1997 “Apart from the evolution of the genetic code, all these transitions involve the coming together of previously independent replicators, to cooperate in a higher-level assembly that reproduces as a single unit.” 3 EC_2018_A12 Natural selection & the evolution of cooperation Cooperation is needed for evolution to construct new levels of organization. -
Effect of Irradiation of the PEM of 1.531211SMJ29 Jeewanu with Clinical Mercury Lamp and Sunlight on the Morphological Features of the Silicon Molybdenum Jeewanu
International Journal of Engineering Research and General Science Volume 4, Issue 4, July-August, 2016 ISSN 2091-2730 Effect of Irradiation of the PEM of 1.531211SMJ29 Jeewanu with Clinical Mercury Lamp and Sunlight on the Morphological Features of the Silicon Molybdenum Jeewanu Deepa Srivastava Department of Chemistry, S.S.Khanna Girls‘ Degree College, Constituent College of Allahabad University, Allahabad, Uttar Pradesh, India E- Mail – [email protected] Abstract— Sterilized aqueous mixture of ammonium molybdate, diammonium hydrogen phosphate, mineral solution and formaldehyde on exposure to sunlight results in the formation of self-sustaining coacervates which were coined as Jeewanu, the autopoetic eukaryote by Bahadur and Ranganayaki. Jeewanu have been analyzed to contain a number of compounds of biological interest. The presence of various enzyme like activities viz., phosphatase, ATP-ase, esterase, nitrogenase have been also been detected in Jeewanu mixture. Gáinti (2003) discussed that Jeewanu possesses a promising configuration similar to protocell-like model. Keywords— Autopoetic, eukaryote, Jeewanu, PEM, sunlight, mercury lamp, morphology, 1.531211SMJ29 INTRODUCTION Sterilized aqueous mixture of ammonium molybdate, diammonium hydrogen phosphate, mineral solution and formaldehyde on exposure to sunlight results in the formation of self-sustaining coacervates which were coined as Jeewanu, the autopoetic eukaryote by Bahadur, K and Ranganayaki, S. in 1970. [1] The photochemical, formation of protocell-like microstructures ―Jeewanu‖ in a laboratory simulated prebiotic atmosphere capable of showing multiplication by budding, growth from within by actual synthesis of material and various metabolic activities has been reported by Bahadur et al. [1, 2, 3, 4, 5, 7, 8] Jeewanu have been analyzed to contain a number of compounds of biological interest viz. -
The Evolutionary Life History of P Transposons: from Horizontal Invaders to Domesticated Neogenes
Chromosoma (2001) 110:148–158 DOI 10.1007/s004120100144 CHROMOSOMA FOCUS Wilhelm Pinsker · Elisabeth Haring Sylvia Hagemann · Wolfgang J. Miller The evolutionary life history of P transposons: from horizontal invaders to domesticated neogenes Received: 5 February 2001 / In revised form: 15 March 2001 / Accepted: 15 March 2001 / Published online: 3 May 2001 © Springer-Verlag 2001 Abstract P elements, a family of DNA transposons, are uct of their self-propagating lifestyle. One of the most known as aggressive intruders into the hitherto uninfected intensively studied examples is the P element of Dro- gene pool of Drosophila melanogaster. Invading through sophila, a family of DNA transposons that has proved horizontal transmission from an external source they useful not only as a genetic tool (e.g., transposon tag- managed to spread rapidly through natural populations ging, germline transformation vector), but also as a model within a few decades. Owing to their propensity for rapid system for investigating general features of the evolu- propagation within genomes as well as within popula- tionary behavior of mobile DNA (Kidwell 1994). P ele- tions, they are considered as the classic example of self- ments were first discovered as the causative agent of hy- ish DNA, causing havoc in a genomic environment per- brid dysgenesis in Drosophila melanogaster (Kidwell et missive for transpositional activity. Tracing the fate of P al. 1977) and were later characterized as a family of transposons on an evolutionary scale we describe differ- DNA transposons -
Constructing Protocells: a Second Origin of Life
04_SteenRASMUSSEN.qxd:Maqueta.qxd 4/6/12 11:45 Página 585 Session I: The Physical Mind CONSTRUCTING PROTOCELLS: A SECOND ORIGIN OF LIFE STEEN RASMUSSEN Center for Fundamental Living Technology (FLinT) Santa Fe Institute, New Mexico USA ANDERS ALBERTSEN, PERNILLE LYKKE PEDERSEN, CARSTEN SVANEBORG Center for Fundamental Living Technology (FLinT) ABSTRACT: What is life? How does nonliving materials become alive? How did the first living cells emerge on Earth? How can artificial living processes be useful for technology? These are the kinds of questions we seek to address by assembling minimal living systems from scratch. INTRODUCTION To create living materials from nonliving materials, we first need to understand what life is. Today life is believed to be a physical process, where the properties of life emerge from the dynamics of material interactions. This has not always been the assumption, as living matter at least since the origin of Hindu medicine some 5000 years ago, was believed to have a metaphysical vital force. Von Neumann, the inventor of the modern computer, realized that if life is a physical process it should be possible to implement life in other media than biochemistry. In the 1950s, he was one of the first to propose the possibilities of implementing living processes in computers and robots. This perspective, while being controversial, is gaining momentum in many scientific communities. There is not a generally agreed upon definition of life within the scientific community, as there is a grey zone of interesting processes between nonliving and living matter. Our work on assembling minimal physicochemical life is based on three criteria, which most biological life forms satisfy. -
Evolutionary Developmental Biology 573
EVOC20 29/08/2003 11:15 AM Page 572 Evolutionary 20 Developmental Biology volutionary developmental biology, now often known Eas “evo-devo,” is the study of the relation between evolution and development. The relation between evolution and development has been the subject of research for many years, and the chapter begins by looking at some classic ideas. However, the subject has been transformed in recent years as the genes that control development have begun to be identified. This chapter looks at how changes in these developmental genes, such as changes in their spatial or temporal expression in the embryo, are associated with changes in adult morphology. The origin of a set of genes controlling development may have opened up new and more flexible ways in which evolution could occur: life may have become more “evolvable.” EVOC20 29/08/2003 11:15 AM Page 573 CHAPTER 20 / Evolutionary Developmental Biology 573 20.1 Changes in development, and the genes controlling development, underlie morphological evolution Morphological structures, such as heads, legs, and tails, are produced in each individual organism by development. The organism begins life as a single cell. The organism grows by cell division, and the various cell types (bone cells, skin cells, and so on) are produced by differentiation within dividing cell lines. When one species evolves into Morphological evolution is driven another, with a changed morphological form, the developmental process must have by developmental evolution changed too. If the descendant species has longer legs, it is because the developmental process that produces legs has been accelerated, or extended over time. -
Kinetic Parameters of Trans Scission by Extended HDV-Like Ribozymes and the Prospect for the Discovery of Genomic Trans-Cleaving Rnas
UC Irvine UC Irvine Previously Published Works Title Kinetic Parameters of trans Scission by Extended HDV-like Ribozymes and the Prospect for the Discovery of Genomic trans-Cleaving RNAs. Permalink https://escholarship.org/uc/item/1894s91p Journal Biochemistry, 57(9) ISSN 0006-2960 Authors Webb, Chiu-Ho T Lupták, Andrej Publication Date 2018-03-01 DOI 10.1021/acs.biochem.7b00789 Supplemental Material https://escholarship.org/uc/item/1894s91p#supplemental Peer reviewed eScholarship.org Powered by the California Digital Library University of California Article Cite This: Biochemistry 2018, 57, 1440−1450 pubs.acs.org/biochemistry Kinetic Parameters of trans Scission by Extended HDV-like Ribozymes and the Prospect for the Discovery of Genomic trans- Cleaving RNAs Chiu-Ho T. Webb†,∥ and Andrej Luptaḱ*,†,‡,§ † Department of Molecular Biology and Biochemistry, University of CaliforniaIrvine, Irvine, California 92697, United States ‡ Department of Pharmaceutical Sciences, University of CaliforniaIrvine, Irvine, California 92697, United States § Department of Chemistry, University of CaliforniaIrvine, Irvine, California 92697, United States *S Supporting Information ABSTRACT: Hepatitis delta virus (HDV)-like ribozymes are self- cleaving catalytic RNAs with a widespread distribution in nature and biological roles ranging from self-scission during rolling-circle replication in viroids to co-transcriptional processing of eukaryotic retrotransposons, among others. The ribozymes fold into a double pseudoknot with a common catalytic core motif and highly variable peripheral domains. Like other self-cleaving ribozymes, HDV-like ribozymes can be converted into trans-acting catalytic RNAs by bisecting the self-cleaving variants at non- essential loops. Here we explore the trans-cleaving activity of ribozymes derived from the largest examples of the ribozymes (drz-Agam-2 family), which contain an extended domain between the substrate strand and the rest of the RNA. -
Downloads/Repeatmaskedgenomes
Kojima Mobile DNA (2018) 9:2 DOI 10.1186/s13100-017-0107-y REVIEW Open Access Human transposable elements in Repbase: genomic footprints from fish to humans Kenji K. Kojima1,2 Abstract Repbase is a comprehensive database of eukaryotic transposable elements (TEs) and repeat sequences, containing over 1300 human repeat sequences. Recent analyses of these repeat sequences have accumulated evidences for their contribution to human evolution through becoming functional elements, such as protein-coding regions or binding sites of transcriptional regulators. However, resolving the origins of repeat sequences is a challenge, due to their age, divergence, and degradation. Ancient repeats have been continuously classified as TEs by finding similar TEs from other organisms. Here, the most comprehensive picture of human repeat sequences is presented. The human genome contains traces of 10 clades (L1, CR1, L2, Crack, RTE, RTEX, R4, Vingi, Tx1 and Penelope) of non-long terminal repeat (non-LTR) retrotransposons (long interspersed elements, LINEs), 3 types (SINE1/7SL, SINE2/tRNA, and SINE3/5S) of short interspersed elements (SINEs), 1 composite retrotransposon (SVA) family, 5 classes (ERV1, ERV2, ERV3, Gypsy and DIRS) of LTR retrotransposons, and 12 superfamilies (Crypton, Ginger1, Harbinger, hAT, Helitron, Kolobok, Mariner, Merlin, MuDR, P, piggyBac and Transib) of DNA transposons. These TE footprints demonstrate an evolutionary continuum of the human genome. Keywords: Human repeat, Transposable elements, Repbase, Non-LTR retrotransposons, LTR retrotransposons, DNA transposons, SINE, Crypton, MER, UCON Background contrast, MER4 was revealed to be comprised of LTRs of Repbase and conserved noncoding elements endogenous retroviruses (ERVs) [1]. Right now, Repbase Repbase is now one of the most comprehensive data- keeps MER1 to MER136, some of which are further bases of eukaryotic transposable elements and repeats divided into several subfamilies. -
Transposable Elements (Transposons)
9.1: Transposable Elements (Transposons) Transposable elements (both active and inactive) occupy approximately half the human genome and a substantially greater fraction of some plant genomes! These movable elements are ubiquitous in the biosphere, and are highly successful in propagating themselves. We now realize that some transposable elements are also viruses, for instance, some retroviruses can integrate into a host genome to form endogenous retroviruses. Indeed, some viruses may be derived from natural transposable elements and vice versa. Since viruses move between individuals, at least some transposable elements can move between genomes (between individuals) as well as within an individual’s genome. Given their prevalence in genomes, the function (if any) of transposable elements has been much discussed but is little understood. It is not even clear whether transposable elements should be considered an integral part of a species’ genome, or if they are successful parasites. They do have important effects on genes and their phenotypes, and they are the subject of intense investigation. Transposition is related to replication, recombination and repair. The process of moving from one place to another involves a type of recombination, insertions of transposable elements can cause mutations, and some transpositions are replicative, generating a new copy while leaving the old copy intact. However, this ability to move is a unique property of transposable elements, and warrants treatment by itself. Properties and effects of transposable elements The defining property of transposable elements is their mobility; i.e. they are genetic elements that can move from one position to another in the genome. Beyond the common property of mobility, transposable elements show considerable diversity.