The Lamarckian Chicken and the Darwinian Egg Yitzhak Pilpel1* and Oded Rechavi2*
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The Evolution of Universal Adaptations of Life Is Driven by Universal Properties of Matter: Energy, Entropy, and Interaction [Version 2; Peer Review: 3 Approved]
F1000Research 2020, 9:626 Last updated: 23 SEP 2021 OPINION ARTICLE The evolution of universal adaptations of life is driven by universal properties of matter: energy, entropy, and interaction [version 2; peer review: 3 approved] Irun R. Cohen 1, Assaf Marron 2 1Department of Immunology, Weizmann Institute of Science, Rehovot, 76100, Israel 2Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, 76100, Israel v2 First published: 18 Jun 2020, 9:626 Open Peer Review https://doi.org/10.12688/f1000research.24447.1 Second version: 30 Jul 2020, 9:626 https://doi.org/10.12688/f1000research.24447.2 Reviewer Status Latest published: 02 Sep 2020, 9:626 https://doi.org/10.12688/f1000research.24447.3 Invited Reviewers 1 2 3 Abstract The evolution of multicellular eukaryotes expresses two sorts of version 3 adaptations: local adaptations like fur or feathers, which characterize (revision) species in particular environments, and universal adaptations like 02 Sep 2020 microbiomes or sexual reproduction, which characterize most multicellulars in any environment. We reason that the mechanisms version 2 driving the universal adaptations of multicellulars should themselves (revision) report report be universal, and propose a mechanism based on properties of matter 30 Jul 2020 and systems: energy, entropy, and interaction. Energy from the sun, earth and beyond creates new arrangements and interactions. version 1 Metabolic networks channel some of this energy to form cooperating, 18 Jun 2020 report report interactive arrangements. Entropy, used here as a term for all forces that dismantle ordered structures (rather than as a physical quantity), acts as a selective force. Entropy selects for arrangements that resist it 1. -
Metazoan Ribosome Inactivating Protein Encoding Genes Acquired by Horizontal Gene Transfer Received: 30 September 2016 Walter J
www.nature.com/scientificreports OPEN Metazoan Ribosome Inactivating Protein encoding genes acquired by Horizontal Gene Transfer Received: 30 September 2016 Walter J. Lapadula1, Paula L. Marcet2, María L. Mascotti1, M. Virginia Sanchez-Puerta3 & Accepted: 5 April 2017 Maximiliano Juri Ayub1 Published: xx xx xxxx Ribosome inactivating proteins (RIPs) are RNA N-glycosidases that depurinate a specific adenine residue in the conserved sarcin/ricin loop of 28S rRNA. These enzymes are widely distributed among plants and their presence has also been confirmed in several bacterial species. Recently, we reported for the first timein silico evidence of RIP encoding genes in metazoans, in two closely related species of insects: Aedes aegypti and Culex quinquefasciatus. Here, we have experimentally confirmed the presence of these genes in mosquitoes and attempted to unveil their evolutionary history. A detailed study was conducted, including evaluation of taxonomic distribution, phylogenetic inferences and microsynteny analyses, indicating that mosquito RIP genes derived from a single Horizontal Gene Transfer (HGT) event, probably from a cyanobacterial donor species. Moreover, evolutionary analyses show that, after the HGT event, these genes evolved under purifying selection, strongly suggesting they play functional roles in these organisms. Ribosome inactivating proteins (RIPs, EC 3.2.2.22) irreversibly modify ribosomes through the depurination of an adenine residue in the conserved alpha-sarcin/ricin loop of 28S rRNA1–4. This modification prevents the binding of elongation factor 2 to the ribosome, arresting protein synthesis5, 6. The occurrence of RIP genes has been exper- imentally confirmed in a wide range of plant taxa, as well as in several species of Gram positive and Gram negative bacteria7–9. -
GENOME BIOLOGY and EVOLUTION (Online ISSN 1759-6653)
GENOME BIOLOGY AND EVOLUTION (Online ISSN 1759-6653) Founding Editor: Takashi Gojobori Editor-in-Chief: William Martin Editorial Assistant: Alison Bentley Editorial Board Names and full contact details for members of the editorial board are available at: www.oxfordjournals.org/our_journals/gbe/editorial_board.html. Information for Authors Information on preparing and submitting manuscripts and a Manuscript Submission Checklist are available at www.oxfordjournals.org/our_journals/gbe/for_authors/. SOCIETY FOR MOLECULAR BIOLOGY AND EVOLUTION www.smbe.org COUNCIL Michael Lynch, President Department of Biology, Indiana University, 1001 E. Third Street, Bloomington, IN 47405 USA. E-mail: [email protected]. Jody Hey, President-Elect Department of Genetics, Rutgers University, 604 Allison Road, Piscataway, NJ 08854 USA. E-mail: [email protected]. Paul Sharp, Past President Institute of Evolutionary Biology, University of Edinburgh, Ashworth Laboratories, West Mains Road, Edinburgh EH9 3JT UK. E-mail: [email protected]. Jianzhi George Zhang, Secretary Department of Ecology and Evolutionary Biology, University of Michigan, 1075 Kraus Natural Science Building, 830 N. University, Ann Arbor, MI 48109-1048 USA. E-mail: [email protected]. John Archibald, Treasurer Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, B3H 1X5 Canada. E-mail: [email protected]. Laura Landweber, Councillor (2007–2009) Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544-1003 USA. E-mail: lfl@princeton.edu. Ziheng Yang, Councillor (2008–2010) Department of Biology, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK. E-mail: [email protected]. Dan Graur, Councillor (2009–2011) Department of Biology and Biochemistry, University of Houston, Houston, Texas 77204-5001 USA. -
Snakemake As a Workflow Engine for Reciprocal BLAST Analyses
Snakemake as a workflow engine for reciprocal BLAST analyses Lukas Becker A thesis presented for the degree of Bachelor of Science Supervisor: Prof. Dr. Gunnar Klau Second Assessor: Dr. Nicolas Schmelling Algorithmic Bioinformatics Heinrich Heine University Düsseldorf Germany 25th February, 2021 Acknowledgments I would like to express my gratitude for Prof. Gunnar Klau whose encouragement and guidance throughout this study has been a great support. Furthermore, I owe special thanks to Dr. Nicolas Schmelling for his invaluable support, constructive feedback and continued assistance in my various questions. Thanks for the opportunity to work on this thesis and the experience to work on this cooperative topic. In addition, I would like to thank Philipp Spohr for his patience with my many questions and his advice and valuable guidance. Thanks. ii Abstract In modern genomic analysis, homology describes the evolutionary relationship between two sequences. In addition to a diverse classification of homology, the key concept for evolutionary and comparative genomics is the dichotomous differentiation of homology into orthologous and paralogous sequences. Sets of orthologous genes are used to obtain information regarding gene functions and phylogenetic relationships because orthologs tend to retain their biolog- ical function. Various methods have been developed in order to identify orthologous genes. Typically, orthologous and paralogous gene relationships are disentangled by measuring and comparing sequence similarities within sequences of interest. More precisely, when search- ing orthologous sequences in different genomes, those sequences will most likely match each other as best hits when performing sequence similarity searches. The resulting sequences are called reciprocal best hits (RBHs). The identification of RBHs is the most common method to infer putative orthologs in comparative genomic studies. -
Virus World As an Evolutionary Network of Viruses and Capsidless Selfish Elements
Virus World as an Evolutionary Network of Viruses and Capsidless Selfish Elements Koonin, E. V., & Dolja, V. V. (2014). Virus World as an Evolutionary Network of Viruses and Capsidless Selfish Elements. Microbiology and Molecular Biology Reviews, 78(2), 278-303. doi:10.1128/MMBR.00049-13 10.1128/MMBR.00049-13 American Society for Microbiology Version of Record http://cdss.library.oregonstate.edu/sa-termsofuse Virus World as an Evolutionary Network of Viruses and Capsidless Selfish Elements Eugene V. Koonin,a Valerian V. Doljab National Center for Biotechnology Information, National Library of Medicine, Bethesda, Maryland, USAa; Department of Botany and Plant Pathology and Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, USAb Downloaded from SUMMARY ..................................................................................................................................................278 INTRODUCTION ............................................................................................................................................278 PREVALENCE OF REPLICATION SYSTEM COMPONENTS COMPARED TO CAPSID PROTEINS AMONG VIRUS HALLMARK GENES.......................279 CLASSIFICATION OF VIRUSES BY REPLICATION-EXPRESSION STRATEGY: TYPICAL VIRUSES AND CAPSIDLESS FORMS ................................279 EVOLUTIONARY RELATIONSHIPS BETWEEN VIRUSES AND CAPSIDLESS VIRUS-LIKE GENETIC ELEMENTS ..............................................280 Capsidless Derivatives of Positive-Strand RNA Viruses....................................................................................................280 -
Is the Germline Immortal and Continuous? a Discussion in Light of Ipscs and Germline Regeneration
Is the Germline Immortal and Continuous? A Discussion in Light of iPSCs and Germline Regeneration 1 1 Kate MacCord and B. Duygu Özpolat 1 - Marine Biological Laboratory, Woods Hole, MA, USA 1 ABSTRACT The germline gives rise to gametes, is the hereditary cell lineage, and is often called immortal and continuous. However, what exactly is immortal and continuous about the germline has recently come under scrutiny. The notion of an immortal and continuous germline has been around for over 130 years, and has led to the concept of a barrier between the germline and soma (the “Weismann barrier”). One repercussion of such a barrier is the understanding that when the germline is lost, soma cannot replace it, rendering the organism infertile. Recent research on induced pluripotent stem cells (iPSCs) and germline regeneration raise questions about the impermeability of the Weismann barrier and the designation of the germline as immortal and continuous. How we conceive of the germline and its immortality shapes what we perceive to be possible in animal biology, such as whether somatic cells contribute to the germline in some metazoans during normal development or regeneration. We argue that reassessing the universality of germline immortality and continuity across all metazoans leads to big and exciting open questions about the germ-soma cell distinction, cell reprogramming, germline editing, and even evolution. 2 1.0 Introduction The germline is the lineage of reproductive cells that includes gametes and their precursors, including primordial germ cells and germline stem cells. Because the germline gives rise to the gametes, it is the hereditary cell lineage, and is ultimately responsible for all cells in an organism’s body, including the next generation of the germline, stem cells, and other somatic cells. -
Origin of the Cell Nucleus, Mitosis and Sex: Roles of Intracellular Coevolution Thomas Cavalier-Smith*
Cavalier-Smith Biology Direct 2010, 5:7 http://www.biology-direct.com/content/5/1/7 RESEARCH Open Access Origin of the cell nucleus, mitosis and sex: roles of intracellular coevolution Thomas Cavalier-Smith* Abstract Background: The transition from prokaryotes to eukaryotes was the most radical change in cell organisation since life began, with the largest ever burst of gene duplication and novelty. According to the coevolutionary theory of eukaryote origins, the fundamental innovations were the concerted origins of the endomembrane system and cytoskeleton, subsequently recruited to form the cell nucleus and coevolving mitotic apparatus, with numerous genetic eukaryotic novelties inevitable consequences of this compartmentation and novel DNA segregation mechanism. Physical and mutational mechanisms of origin of the nucleus are seldom considered beyond the long- standing assumption that it involved wrapping pre-existing endomembranes around chromatin. Discussions on the origin of sex typically overlook its association with protozoan entry into dormant walled cysts and the likely simultaneous coevolutionary, not sequential, origin of mitosis and meiosis. Results: I elucidate nuclear and mitotic coevolution, explaining the origins of dicer and small centromeric RNAs for positionally controlling centromeric heterochromatin, and how 27 major features of the cell nucleus evolved in four logical stages, making both mechanisms and selective advantages explicit: two initial stages (origin of 30 nm chromatin fibres, enabling DNA compaction; and firmer attachment of endomembranes to heterochromatin) protected DNA and nascent RNA from shearing by novel molecular motors mediating vesicle transport, division, and cytoplasmic motility. Then octagonal nuclear pore complexes (NPCs) arguably evolved from COPII coated vesicle proteins trapped in clumps by Ran GTPase-mediated cisternal fusion that generated the fenestrated nuclear envelope, preventing lethal complete cisternal fusion, and allowing passive protein and RNA exchange. -
Reticulate Evolution Everywhere
Reticulate Evolution Everywhere Nathalie Gontier Abstract Reticulation is a recurring evolutionary pattern found in phylogenetic reconstructions of life. The pattern results from how species interact and evolve by mechanisms and processes including symbiosis; symbiogenesis; lateral gene transfer (that occurs via bacterial conjugation, transformation, transduction, Gene Transfer Agents, or the movements of transposons, retrotransposons, and other mobile genetic elements); hybridization or divergence with gene flow; and infec- tious heredity (induced either directly by bacteria, bacteriophages, viruses, pri- ons, protozoa and fungi, or via vectors that transmit these pathogens). Research on reticulate evolution today takes on inter- and transdisciplinary proportions and is able to unite distinct research fields ranging from microbiology and molecular genetics to evolutionary biology and the biomedical sciences. This chapter sum- marizes the main principles of the diverse reticulate evolutionary mechanisms and situates them into the chapters that make up this volume. Keywords Reticulate evolution · Symbiosis · Symbiogenesis · Lateral Gene Transfer · Infectious agents · Microbiome · Viriome · Virolution · Hybridization · Divergence with gene flow · Evolutionary patterns · Extended Synthesis 1 Reticulate Evolution: Patterns, Processes, Mechanisms According to the Online Etymology Dictionary (http://www.etymonline.com), the word reticulate is an adjective that stems from the Latin words “re¯ticulātus” (having a net-like pattern) and re¯ticulum (little net). When scholars identify the evolution of life as being “reticulated,” they first and foremost refer to a recurring evolutionary pattern. N. Gontier (*) AppEEL—Applied Evolutionary Epistemology Lab, University of Lisbon, Lisbon, Portugal e-mail: [email protected] © Springer International Publishing Switzerland 2015 1 N. Gontier (ed.), Reticulate Evolution, Interdisciplinary Evolution Research 3, DOI 10.1007/978-3-319-16345-1_1 2 N. -
New Ideas in Evolutionary Biology: from NDMS to EES Sy Garte Sy Garte
Article New Ideas in Evolutionary Biology: From NDMS to EES Sy Garte Sy Garte The neo-Darwinian modern synthesis (NDMS) has been the bedrock of evolution- ary theory for many decades. But the NDMS has proven limited and out of date with respect to several areas of biological research. A new extended evolutionary synthesis (EES), which takes into account more complex interactions between genomes, the cell and the environment, allows for a reexamination of many of the assumptions of the NDMS. To the standard paradigm of slow accumulation of random point mutations as the major mechanism of biological variation must now be added new data and concepts of symbiosis, gene duplication, horizontal gene transfer, retrotransposition, epigenetic control networks, niche construction, stress-directed mutations, and large-scale reengi- neering of the genome in response to environmental stimuli. There may be implications for Christian faith in this opening of evolutionary theory to a broader and more exciting view of Darwin’s great theory. heoretical evolutionary biology The Neo-Darwinian has been undergoing a crescendo Synthesis of transformations in recent years. T In the middle of the twentieth century, After a long period of general acceptance even before the chemical nature of the of the traditional paradigm for how evo- gene was known, biologists were exam- lution works, new data and concepts from ining mutations in experimental systems many fi elds of biological science have of bacteria in order to answer questions begun to challenge the status quo of evo- about purpose and chance in mutation lutionary theory. There is no question that production. -
A Fundamentally New Perspective on the Origin and Evolution of Life Shi
A Fundamentally New Perspective on the Origin and Evolution of Life Shi V. Liu Eagle Institute of Molecular Biology Apex, NC 27502 USA [email protected] Motto Criticism and attempted “falsification” are essential parts of science. - Philip J. Darlington, Jr. (1904-1983) Abstract Darwin’s hypothesis that all extant life forms are descendants of a last common ancestor cell and diversification of life forms results from gradual mutation plus natural selection represents a mainstream view that has influenced biology and even society for over a century. However, this Darwinian view on life is contradicted by many observations and lacks a plausible physico-chemical explanation. Strong evidence suggests that the common ancestor cell hypothesis is the most fundamental flaw of Darwinism. By contrast, a totally different perspective on origin and evolution of life claims that cellular life forms were descendants of already diversified acellular life forms. Independently originated life forms evolve largely in some parallel ways even though they also interact with each other. Some evolutionary “gaps” naturally exist among evolutionary lines. Similarity may not be the only result of phylogenetic inheritance but may be a result of a convergent mechanism of origin and evolution. Evolution is not a random process but follows some basic physico-chemical principles as a result of the interplay of both energy and entropy on matter. Next year will be the 150th anniversary of the publication of Darwin’s famous book “On the Origin of Species by Means of natural Selection or the Preservation of Favored Races in the Struggle for Life” (1) and a celebration for the 200th birthday of a most influential biological scientist of all time (2, 3). -
Report for the Academic Year 1999
l'gEgasag^a3;•*a^oggMaBgaBK>ry^vg^.g^._--r^J3^JBgig^^gqt«a»J^:^^^^^ Institute /or ADVANCED STUDY REPORT FOR THE ACADEMIC YEAR 1998-99 PRINCETON • NEW JERSEY HISTORICAL STUDIES^SOCIAl SC^JCE LIBRARY INSTITUTE FOR ADVANCED STUDY PRINCETON, NEW JERSEY 08540 Institute /or ADVANCED STUDY REPORT FOR THE ACADEMIC YEAR 1 998 - 99 OLDEN LANE PRINCETON • NEW JERSEY • 08540-0631 609-734-8000 609-924-8399 (Fax) http://www.ias.edu Extract from the letter addressed by the Institute's Founders, Louis Bamberger and Mrs. FeUx Fuld, to the Board of Trustees, dated June 4, 1930. Newark, New Jersey. It is fundamental m our purpose, and our express desire, that in the appointments to the staff and faculty, as well as in the admission of workers and students, no account shall be taken, directly or indirectly, of race, religion, or sex. We feel strongly that the spirit characteristic of America at its noblest, above all the pursuit of higher learning, cannot admit of any conditions as to personnel other than those designed to promote the objects for which this institution is established, and particularly with no regard whatever to accidents of race, creed, or sex. ni' TABLE OF CONTENTS 4 • BACKGROUND AND PURPOSE 7 • FOUNDERS, TRUSTEES AND OFFICERS OF THE BOARD AND OF THE CORPORATION 10 • ADMINISTRATION 12 • PRESENT AND PAST DIRECTORS AND FACULTY 15 REPORT OF THE CHAIRMAN 18 • REPORT OF THE DIRECTOR 22 • OFFICE OF THE DIRECTOR - RECORD OF EVENTS 27 ACKNOWLEDGMENTS 41 • REPORT OF THE SCHOOL OF HISTORICAL STUDIES FACULTY ACADEMIC ACTIVITIES MEMBERS, VISITORS, -
A Two Days Mini Course by Prof. Eugene Koonin-Chance And
A two days mini course by Prof. Eugene Koonin will be given at Apr 23-4 at the Inst. of Evolution and the Department of Evolutionary and Environmental Biology at the Univ. of Haifa The mini course will include two meetings, three hours each. Talks are targeted not necessarily and specifically at evolutionary biologists, rather at the wider spectrum of biologists and even exact scientists. People wishing to participate in specific talks are welcome. Please find specific details below. Further information can be obtained from Sagi Snir Course Title: Chance and Necessity in Genome Evolution Speaker: Eugene V. Koonin, National Center for Biotechnology Information, NIH, Bethesda, USA Time: April 23-4, 10:00-13:00. Location: The seminar room in the new labs complex (located at the former Student Union offices, no 11 in the map) http://multimedia.haifa.ac.il/campus_map/ The course will be broken down into six lectures, so people unable to attend all lectures can choose based on interest/availability Day 1 (Tuesday) 1. Overview of comparative and evolutionary genomics 2. The "laws" of genome and phenome evolution 3. The Tree of Life, the three domains, and the origin of eukaryotes Day 2 (Wednesday) 4. Evolution of viruses and virus-host arms race as a fundamental factor of evolution 5. Evolution of genomic complexity 6. The interplay of randomness and adaption in genome evolution and the overhaul of the theory of evolution Abstract: These lectures aim at presenting a panoramic view of today’s Evolutionary Biology in light of the results of Comparative Genomics and Systems Biology.