In the Company of Microbes Ten Years of Small Things Considered Elio Schaechter Artwork by Judith Schaechter In the Company of Microbes Ten Years of Small Things Considered Washington, DC Copyright © 2016 American Society for Microbiology. All rights reserved. No part of this publication may be reproduced or transmitted in whole or in part or reused in any form or by any means, electronic or mechanical, including photocopying and recording, or by any information storage and retrieval system, without permission in writing from the publisher. Disclaimer: To the best of the publisher’s knowledge, this publication provides information concerning the subject matter covered that is accurate as of the date of publication. The publisher is not providing legal, medical, or other professional services. Any reference herein to any specific commercial products, procedures, or services by trade name, trademark, manufacturer, or otherwise does not constitute or imply endorsement, recommendation, or favored status by the American Soci- ety for Microbiology (ASM). The views and opinions of the author(s) expressed in this publication do not necessarily state or reflect those of ASM, and they shall not be used to advertise or endorse any product. Library of Congress Cataloging-in-Publication Data Names: Schaechter, Moselio, editor. | Schaechter, Judith, 1961- illustrator. Title: In the company of microbes : ten years of Small Things Considered / edited by Elio Schaechter ; artwork by Judith Schaechter. Description: Washington, DC : ASM Press, [2016] | ?2016 | Includes bibliographical references. Identifiers: LCCN 2016011177 | ISBN 9781555819590 (pbk.) Subjects: LCSH: Microbiology–Blogs. | Microorganisms–Blogs. Classification: LCC QR56 .I5 2016 | DDC 576--dc23 LC record available at http://lccn.loc.gov/2016011177 10 9 8 7 6 5 4 3 2 1 All Rights Reserved Printed in the United States of America Address editorial correspondence to ASM Press, 1752 N St., N.W., Washington, DC 20036-2904, USA Send orders to ASM Press, P.O. Box 605, Herndon, VA 20172, USA Phone: 800-546-2416; 703-661-1593; Fax: 703-661-1501 E-mail: [email protected] Online: http://estore.asm.org Cover image: Judith Schaechter Design: Lou Moriconi Table of Contents Contributors.................................................................................. x Introduction................................................................................. xi Preface.........................................................................................xiii Acknowledgments.......................................................................xv What Do We Mean by a Talmudic Question?.........................xvi Part 1: The View from Here 1 Of Ancient Curses, Microbes, and the ASM..................................... 3 Bonnie L. Bassler 2 On the Evolution of the Genetic Code............................................. 6 Charles Yanofsky 3 Microbes Touch Everything.............................................................. 8 Tim Donohue 4 Getting a Handle on Cell Organization ..........................................11 Franklin M. Harold 5 The Age of Imaging........................................................................ 16 Elio 6 Bacillus subtilis: Wild and Tame................................................... 19 Richard Losick 7 The Tyranny of Phylogeny: An Exhortation................................... 22 Elio 8 Virus in the Room.......................................................................... 24 Welkin Johnson 9 Feynman Said “Just Look at the Thing!”........................................ 27 Jan Spitzer iv • In the Company of Microbes 10 Self-Assembly For Me..................................................................... 34 Elio 11 On the Definition of Prokaryotes................................................... 37 Nanne Nanninga 12 The Microbial Nature of Humans................................................... 42 Maureen O’Malley 13 Good Writing Beats Bad Writing, Most Any Day ........................... 47 Elio 14 Finally, Farewell to “Stamp Collecting”.......................................... 52 Christoph Weigel Part 2: Accounts of the Past 15 Esther Lederberg: Pioneer of Bacterial Genetics ......................... 59 Mercé Piqueras 16 How Proteomics Got Started ......................................................... 66 Fred Neidhardt 17 Did van Leeuwenhoek Observe Yeast Cells in 1680? ................... 72 Nanne Nanninga 18 The Louse and the Vaccine ........................................................... 76 Elio 19 The Ten-Minute Leeuwenhoek Microscope .................................. 80 Patrick Keeling 20 Microbiology in the Andes: Ancient and Unexpected .................. 84 Elio 21 Dr. Rous’s Prize-Winning Chicken ................................................. 87 Welkin Johnson v 22 The Two Quantitative Steps in the Biology Growth Curve ......................................................... 90 Elio 23 A Tale of Centenarians ................................................................. 93 Claudio Schazzocchio 24 A Failed Experiment ..................................................................... 99 Elio 25 “Microbe Hunters” by Paul DeKruif: A Major Force in Microbiological History .....................................104 Elio 26 Fecal Transplants in the “Good Old Days” ...................................106 Stanley Falkow 27 Requiem for a Machine ............................................................... 110 Elio 28 Mad Dogs and Microbiologists .....................................................11 3 William C. Summers 29 Joshua Lederberg and the “Cellularity” of Bacteria ....................11 8 Elio Part 3: Small Wonders 30 Where Art Thou, O Nucleoid? ..................................................... 123 Conrad Woldringh 31 Teaching E. coli to Endocytose .................................................... 126 Elio 32 The Awesomest Thing in Biology ................................................ 130 Elio 33 Let’s Not Forget Acetabularia ...................................................... 134 Elio 34 The Fastest Flights in Nature........................................................ 139 Elio vi • In the Company of Microbes 35 Fungal Alchemy: Using Radiation as a Source of Energy.............141 Elio 36 Arms and the Fungus................................................................... 143 Elio 37 Bacterial Hopanoids: The Lipids That Last Forever..................... 146 Elio 38 A Bacterium Learns Long Division............................................... 150 Nanne Nanninga 39 Commuting to Work..................................................................... 153 Elio Part 4: On Being a Microbiologist 40 Directed Science, Curiosity-Driven Science, and Striking the Balance.............................................................. 159 Jeff F. Miller 41 The Gender Bias of Science Faculty............................................. 163 Vincent Racaniello 42 The Excitement of Clinical Microbiology..................................... 166 Elio 43 The Bacterial Chromosome: A Physical Biologist’s Apology. A Perspective...............................171 Suckjoon Jun 44 Whose Planet Is It Anyway?......................................................... 177 Elio 45 If Microbes Could Tweet................................................................181 Daniel P. Haeusser 46 State Microbes.............................................................................. 183 Elio 47 Recalling the Good in the Good Old Days .................................. 187 Elio vii 48 The Attendee’s Guide to Scientific Meetings............................... 189 Julian Davies Part 5: Personal Notes 49 The Encyclopedia and I................................................................ 195 Elio 50 The Guild...................................................................................... 198 Elio 51 The Magasanik Paradox................................................................ 200 Elio Part 6: The Ways of Microbes 52 The Parvome................................................................................. 205 Julian Davies 53 The World Is Pleiotropic............................................................... 208 Elio 54 Constructing a Synthetic Mycoplasma.......................................... 211 Shmuel Razin 55 By Chance and Necessity: The Role of the Cytoskeleton in the Genesis of Eukaryotes.........214 Daniel P. Haeusser 56 The Gram Stain: Its Persistence and Its Quirks.............................221 Elio 57 On the Continuity of Biological Membranes............................... 226 Franklin M. Harold 58 Energetics of the Eukaryotic Edge............................................... 223 Franklin M. Harold 59 The Road to Microbial Endocrinology ......................................... 238 Mark Lyte viii • In the Company of Microbes 60 Begetting the Eukarya: An Unexpected Light.............................. 244 Franklin M. Harold 61 The Higgs Boson and Biology....................................................... 253 Elio 62 The Power of Fungal Genetics: Cassava for Food Security and Sustainability in Colombia......... 257 Chris Condaya Peter Geoghan 63 Why Is It So Hard to Make an HIV Vaccine?................................. 259 John Coffin 64 Measuring Up............................................................................... 263 Jamie Henzy Part 7: Teaching Things 65 On Teaching ................................................................................ 267 Stanley Falkow