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Nothing in Biology Makes Sense Except in the Light of Evolution: Pattern, Pro Cess, and the Evidence
Nothing in Biology Makes Sense Except in the Light of Evolution: Pattern, Pro cess, and the Evidence Jonathan B. Losos Evolutionary biology is unusual: unlike any other science, evolution- ary biologists study a phenomenon that some people do not think exists. Consider chemistry, for example; it is unlikely that anyone does not believe in the existence of chemical reactions. Ditto for the laws of physics. Even within biology, no one believes that cells do not exist nor that DNA is a fraud. But public opinion polls consistently show that a majority of the American public is either unsure about or does not believe that life has evolved through time. For example, a Gallup poll taken repeatedly over the past twenty years indicates that as much as 40 percent of the population believes that the Bible is liter- ally correct. When I teach evolutionary biology, I focus on the ideas about how evolution works, rather than on the empirical record of how species have changed through time. However, for one lecture period I make an exception, and in some respects I consider this the most important lecture of the semester. Sad as I fi nd it to be, most of my students will not go on to become evolutionary biologists. Rather, they will become leaders in many diverse aspects of society: doctors, lawyers, business- people, clergy, and artists; people to whom others will look for guid- ance on matters of knowledge and science. For this reason, although I devote my course to a detailed understanding of the evolutionary pro cess, I consider it vitally important that my students understand why it is that almost all biologists fi nd the evidence that evolution has occurred— and continues to occur— to be overwhelming. -
The Fish That Crawled out of the Water
Published online 5 April 2006 | Nature | doi:10.1038/news060403-7 News The fish that crawled out of the water A newly found fossil links fish to land-lubbers. Rex Dalton A crucial fossil that shows how animals crawled out from the water, evolving from fish into land-loving animals, has been found in Canada. The creature, described today in Nature1,2, lived some 375 million years ago. Palaeontologists are calling the specimen from the Devonian a true 'missing link', as it helps to fill in a gap in our understanding of how fish developed legs for land mobility, before eventually evolving into modern animals including mankind. Several samples of the fish-like tetrapod, named Tiktaalik roseae, were “Tetrapods did not so much discovered by Edward Daeschler of the Academy of Natural Sciences in Philadelphia, Pennsylvania, Neil Shubin of the University of Chicago in conquer the land, The fossilized remains of as escape from the Illinois, Farish Jenkins of Harvard University in Cambridge, Massachusetts Tiktaalik show a crocodile-like water.” and colleagues. creature with joints in its front arms. The crew found the samples in a river delta on Ellesmere Island in Arctic credit Ted Daeschler Canada; these included a near-complete front half of a fossilized skeleton of a crocodile-like creature, whose skull is some 20 centimetres long. The beast has bony scales and fins, but the front fins are on their way to becoming limbs; they have the internal skeletal structure of an arm, including elbows and wrists, but with fins instead of clear fingers. The team is still looking for more complete specimens to get a better picture of hind part of the animal. -
James A. Mccloskey, Jr
CHEMICAL HERITAGE FOUNDATION JAMES A. MCCLOSKEY, JR. Transcript of Interviews Conducted by Michael A. Grayson at the McCloskeys’ Home Helotes, Texas on 19 and 20 March 2012 (With Subsequent Corrections and Additions) James A. McCloskey, Jr. ACKNOWLEDGMENT This oral history is one in a series initiated by the Chemical Heritage Foundation on behalf of the American Society for Mass Spectrometry. The series documents the personal perspectives of individuals related to the advancement of mass spectrometric instrumentation, and records the human dimensions of the growth of mass spectrometry in academic, industrial, and governmental laboratories during the twentieth century. This project is made possible through the generous support of the American Society for Mass Spectrometry. This oral history is designated Free Access. Please note: Users citing this interview for purposes of publication are obliged under the terms of the Chemical Heritage Foundation (CHF) Center for Oral History to credit CHF using the format below: James A. McCloskey, Jr., interview by Michael A. Grayson at the McCloskeys’ home, Helotes, Texas, 19-20 March 2012 (Philadelphia: Chemical Heritage Foundation, Oral History Transcript # 0702). Chemical Heritage Foundation Center for Oral History 315 Chestnut Street Philadelphia, Pennsylvania 19106 The Chemical Heritage Foundation (CHF) serves the community of the chemical and molecular sciences, and the wider public, by treasuring the past, educating the present, and inspiring the future. CHF maintains a world-class collection of materials that document the history and heritage of the chemical and molecular sciences, technologies, and industries; encourages research in CHF collections; and carries out a program of outreach and interpretation in order to advance an understanding of the role of the chemical and molecular sciences, technologies, and industries in shaping society. -
The Great-Grandmother of LUCA (Last Universal Common Ancestor)
Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 4 June 2018 doi:10.20944/preprints201806.0035.v1 Be introduced to the First Universal Common Ancestor (FUCA): the great-grandmother of LUCA (Last Universal Common Ancestor) Francisco Prosdocimi1*, Marco V José2 and Sávio Torres de Farias3* 1 Laboratório de Biologia Teórica e de Sistemas, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil. 2 Theoretical Biology Group, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510 CDMX, Mexico. 3 Laboratório de Genética Evolutiva Paulo Leminsk, Departamento de Biologia Molecular, Universidade Federal da Paraíba, João Pessoa, Paraíba, Brasil. * Correspondence: [email protected]; [email protected] Abstract The existence of a common ancestor to all living organisms in Earth is a necessary corollary of Darwin idea of common ancestry. The Last Universal Common Ancestor (LUCA) has been normally considered as the ancestor of cellular organisms that originated the three domains of life: Bacteria, Archaea and Eukarya. Recent studies about the nature of LUCA indicate that this first organism should present hundreds of genes and a complex metabolism. Trying to bring another of Darwin ideas into the origins of life discussion, we went back into the prebiotic chemistry trying to understand how LUCA could be originated 1 © 2018 by the author(s). Distributed under a Creative Commons CC BY license. Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 4 June 2018 doi:10.20944/preprints201806.0035.v1 under gradualist assumptions. Along this line of reasoning, it became clear to us that the definition of another ancestral should be of particular relevance to the understanding about the emergence of biological systems. -
Beyond the Big Bang • the Amazon's Lost Civilizations • the Truth
SFI Bulletin winter 2006, vol. 21 #1 Beyond the Big Bang • The Amazon’s Lost Civilizations • The Truth Behind Lying The Bulletin of the Santa Fe Institute is published by SFI to keep its friends and supporters informed about its work. The Santa Fe Institute is a private, independent, multidiscipli- nary research and education center founded in 1984. Since its founding, SFI has devoted itself to creating a new kind of sci- entific research community, pursuing emerging synthesis in science. Operating as a visiting institution, SFI seeks to cat- alyze new collaborative, multidisciplinary research; to break down the barriers between the traditional disciplines; to spread its ideas and methodologies to other institutions; and to encourage the practical application of its results. Published by the Santa Fe Institute 1399 Hyde Park Road Santa Fe, New Mexico 87501, USA phone (505) 984-8800 fax (505) 982-0565 home page: http://www.santafe.edu Note: The SFI Bulletin may be read at the website: www.santafe.edu/sfi/publications/Bulletin/. If you would prefer to read the Bulletin on your computer rather than receive a printed version, contact Patrisia Brunello at 505/984-8800, Ext. 2700 or [email protected]. EDITORIAL STAFF: Ginger Richardson Lesley S. King Andi Sutherland CONTRIBUTORS: Brooke Harrington Janet Yagoda Shagam Julian Smith Janet Stites James Trefil DESIGN & PRODUCTION: Paula Eastwood PHOTO: ROBERT BUELTEMAN ©2004 BUELTEMAN PHOTO: ROBERT SFI Bulletin Winter 2006 TOCtable of contents 3 A Deceptively Simple Formula 2 How Life Began 3 From -
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. -
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. -
Farish A. Jenkins Jr (1940–2012) Palaeontologist, Anatomist, Explorer and Artist
COMMENT OBITUARY Farish A. Jenkins Jr (1940–2012) Palaeontologist, anatomist, explorer and artist. ith a rifle strapped to his back nearly a century’s worth of speculation about a serendipitous expansion of his research each summer, a scalpel in his functional anatomy that had been based on programme to include other tetrapod hand each autumn and the eyes fossils alone. groups. In the 1990s and 2000s, Jenkins used Wof an artist throughout the year, Farish Jenkins’s research output was as systematic the same approach to open up the Triassic Jenkins Jr seamlessly blended expeditionary as his military training had been. During the rocks of Greenland and the Devonian palaeontology with experimental sediments of Arctic Canada to anatomy to establish how animals palaeontological discovery. He evolved to walk, run, jump and fly. uncovered haramiyids (some of the Jenkins, who died of com- earliest mammals) in the Triassic plications from pneumonia on rocks and Tiktaalik (a genus of lobe- 11 November, was raised in Rye, finned fish) in the Devonian ones. New York. As a child, he showed Jenkins was president of the no obvious draw towards a life of Society of Vertebrate Paleontology science and exploration. But two in 1981–82, and he received its experiences transformed him. While Romer-Simpson Medal for life- S. KREITER/BOSTON GLOBE VIA GETTY VIA GETTY GLOBE S. KREITER/BOSTON studying philosophy at Princeton time achievement in 2009. He will University in New Jersey in the early be remembered by generations 1960s, Jenkins spent a summer as an of undergraduates, graduate and undergraduate assistant to Glenn medical students and assistant Lowell Jepsen. -
Signature of Controversy
I n “In this volume Granville Sewell provides “As the debate over intelligent design grows T delightful and wide-ranging commentary on increasingly heated... it is refreshing to find a HE the origins debate and intelligent design... discussion of the topic that is calm, thoughtful, Sewell provides much needed clarity on topics and far-ranging, with no sense of having to B e ignature f that are too often misunderstood. His discussion advance an agenda or decimate the opposition. G I S o of the commonly confused problem of entropy In this regard, Granville Sewell’s In the NNI is a must read.” Beginning succeeds brilliantly.” Cornelius G. Hunter, Ph.D. William A. Dembski, Ph.D. N author of The Design Inference author of Science’s Blind Spot G ontroversy A N c In this wide-ranging collection of essays on origins, mathematician Granville Sewell looks at the D big bang, the fine-tuning of the laws of physics, and the evolution of life. He concludes that while O there is much in the history of life that seems to suggest natural causes, there is nothing to support THER Responses to critics of signature in the cEll Charles Darwin’s idea that natural selection of random variations can explain major evolutionary E S advances (“easily the dumbest idea ever taken seriously by science,” he calls it). Sewell explains S A Y why evolution is a fundamentally different and much more difficult problem than others solved s ON by science, and why increasing numbers of scientists are now recognizing what has long been I obvious to the layman, that there is no explanation possible without design. -
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 -
Qnas with Neil Shubin
QNAS QNAS QnAs with Neil Shubin Prashant Nair “ ” Science Writer with a four wheel drive, such as animals that walk on land using limbs. PNAS: Your 2006 description of Tiktaalik furnished a view of the animal’sfrontend. From the rust-brown sediments of long-dried their saga of evolution in his PNAS Inau- Why did it take so long to disinter and de- streams that once rumbled through the rug- gural Article (1). scribe the pelvic appendage? ’ PNAS: Your discovery of Tiktaalik’spelvic ged terrain of Canada s Ellesmere Island, a Shubin: We had collected two blocks of appendage addresses a longstanding conun- team of paleontologists unearthed in 2004 specimens in 2004, one of which contained fi drum in the evolution of locomotion in the fossils of a 375 million-year-old species of sh the front end of the Tiktaalik reference spec- animal kingdom: the contrast between move- that may have nearly crossed an evolutionary imen described in the 2006 papers. We did Tiktaalik roseae ment using fins in the front of the body and Rubicon. Named ,thenow- not look at the second block right away, movement using appendages in the front and extinct animal has come to represent an in- mainly because it didn’tseemtocontain back. Can you explain the evolutionary sig- termediate link between fish and amphibians, much bone and because we had collected nificance of the distinction between these its features likely enabling a leap from water it for the sake of completeness. It took us forms of locomotion? to land. Led by National Academy of Sciences a number of years to prepare, study, and Shubin: Limbed vertebrates, or terapods, member Neil Shubin, a paleontologist at the draw conclusions about this pelvic structure, have four appendages, two in the front and University of Chicago, the team described the found in the second block, partly because the two in the back. -
Neil Shubin '82 Brings out the Fish in All of Us
ANDRES ALONSO ’79 5 MINUTES WITH … CHARLES ARDAI ’91 REFORMS BALTIMORE’S HISTORY PROFESSOR BRINGS PULP FICTION SCHOOL BUREAUCRACY MAE NGAI ’98 GSAS TO TODAY’S READERS PAGE 22 PAGE 11 PAGE 24 Columbia College March/April 2011 TODAY Neil Shubin ’82 Brings Out the Fish in All of Us Shubin, a paleontologist and evolutionary biologist, co-led a team that discovered evidence of the pivotal shift from aquatic to terrestrial life. ust another J membership perk. Meet. Dine. Entertain. Join the Columbia Club and access state-of-the-art meeting rooms for your conferences and events. For more information or to apply, visit www.columbiaclub.org or call (212) 719-0380. The Columbia University Club of New York in residence at 15 West 43 St. New York, N Y 10036 Columbia’s SocialIntellectualCulturalRecreationalProfessional Resource in Midtown. Columbia College Today Contents 22 12 24 7 56 18 COVER STORY ALUMNI NEWS DEPARTMENTS G O FISH 27 O BITUARIES 2 LETTERS TO THE 12 Paleontologist and evolutionary biologist Neil Shubin 27 Joseph D. Coffee Jr. ’41 EDITOR ’82 brings out the fish in all of us. 28 Garland E. Wood ’65 3 ITHIN THE AMILY By Nathalie Alonso ’08 W F 30 B OOKSHEL F 4 AROUND THE QUADS FEATURES Featured: Adam Gidwitz ’04 4 turns classic folklore on its Northwest Corner Building Opens COLUMBIA FORUM ear with his new children’s 18 book, A Tale Dark & Grimm. 5 Rose, Jones Join In an excerpt from his book How Soccer Explains the College Senior Staff World: An Unlikely Theory of Globalization, Franklin 32 LASS OTES 6 Creed To Deliver Foer ’96 explains how one soccer club’s destiny was C N A LUMNI PRO F ILES Class Day Address shaped by European anti-Semitism.