Oral History Interview with Michael Ashburner (B
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
Applied Category Theory for Genomics – an Initiative
Applied Category Theory for Genomics { An Initiative Yanying Wu1,2 1Centre for Neural Circuits and Behaviour, University of Oxford, UK 2Department of Physiology, Anatomy and Genetics, University of Oxford, UK 06 Sept, 2020 Abstract The ultimate secret of all lives on earth is hidden in their genomes { a totality of DNA sequences. We currently know the whole genome sequence of many organisms, while our understanding of the genome architecture on a systematic level remains rudimentary. Applied category theory opens a promising way to integrate the humongous amount of heterogeneous informations in genomics, to advance our knowledge regarding genome organization, and to provide us with a deep and holistic view of our own genomes. In this work we explain why applied category theory carries such a hope, and we move on to show how it could actually do so, albeit in baby steps. The manuscript intends to be readable to both mathematicians and biologists, therefore no prior knowledge is required from either side. arXiv:2009.02822v1 [q-bio.GN] 6 Sep 2020 1 Introduction DNA, the genetic material of all living beings on this planet, holds the secret of life. The complete set of DNA sequences in an organism constitutes its genome { the blueprint and instruction manual of that organism, be it a human or fly [1]. Therefore, genomics, which studies the contents and meaning of genomes, has been standing in the central stage of scientific research since its birth. The twentieth century witnessed three milestones of genomics research [1]. It began with the discovery of Mendel's laws of inheritance [2], sparked a climax in the middle with the reveal of DNA double helix structure [3], and ended with the accomplishment of a first draft of complete human genome sequences [4]. -
Gene Prediction: the End of the Beginning Comment Colin Semple
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by PubMed Central http://genomebiology.com/2000/1/2/reports/4012.1 Meeting report Gene prediction: the end of the beginning comment Colin Semple Address: Department of Medical Sciences, Molecular Medicine Centre, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK. E-mail: [email protected] Published: 28 July 2000 reviews Genome Biology 2000, 1(2):reports4012.1–4012.3 The electronic version of this article is the complete one and can be found online at http://genomebiology.com/2000/1/2/reports/4012 © GenomeBiology.com (Print ISSN 1465-6906; Online ISSN 1465-6914) Reducing genomes to genes reports A report from the conference entitled Genome Based Gene All ab initio gene prediction programs have to balance sensi- Structure Determination, Hinxton, UK, 1-2 June, 2000, tivity against accuracy. It is often only possible to detect all organised by the European Bioinformatics Institute (EBI). the real exons present in a sequence at the expense of detect- ing many false ones. Alternatively, one may accept only pre- dictions scoring above a more stringent threshold but lose The draft sequence of the human genome will become avail- those real exons that have lower scores. The trick is to try and able later this year. For some time now it has been accepted increase accuracy without any large loss of sensitivity; this deposited research that this will mark a beginning rather than an end. A vast can be done by comparing the prediction with additional, amount of work will remain to be done, from detailing independent evidence. -
The Theorist Ridley Makes No Mention of a Meeting She Had Then with the Physicist Alexander Stokes and a Half a Dozen Scientists and Laboratories to Solve
NATURE|Vol 443|26 October 2006 AUTUMN BOOKS the spring of 1950 (not in December, as Ridley writes). She joined the lab in January 1951, and The theorist Ridley makes no mention of a meeting she had then with the physicist Alexander Stokes and a half a dozen scientists and laboratories to solve. graduate student, Raymond Gosling, at which Francis Crick: Discoverer of the Crick himself did very little of the laboratory John Randall, the lab’s director, gave her a sup- Genetic Code work. Rather, he was the explicator, the arbiter, ply of the best DNA they had and appointed by Matt Ridley the taskmaster. Gosling her assistant. Crucially, Wilkins was HarperCollins: 2006. 213 pp. £12.95, $19.95 Crick was above all the theorist — and that’s away on vacation. Franklin had every reason Horace Freeland Judson the unifying thread. Not just with the coding to think the DNA was exclusively hers. When Any biographer of Francis Crick faces a dif- problem but throughout his career, Crick was Wilkins returned and expected to collabo- ficult problem: he was the greatest biologist the one who put other scientists’ thoughts in rate with her, she shut him out. He grumbled of the latter half of the twentieth century, yet order. He soaked up data, mostly other people’s, about her to Crick and Watson, and in Feb- his life was curiously one-dimensional. It was but saw beyond the data to their meaning, their ruary 1953 he notoriously showed Watson an intensely concentrated but narrowly focused. shape, their implications. He found principles, X-ray diagram she had obtained — which they By far the most important part of his life was and did it with a preternatural clarity of mind interpreted as she had failed to do. -
Fizzling the Plutonium Economy: Origins of the April 1977 Carter Administration Fuel Cycle Policy Transition
Fizzling the Plutonium Economy: Origins of the April 1977 Carter Administration Fuel Cycle Policy Transition The Harvard community has made this article openly available. Please share how this access benefits you. Your story matters Citation Williams, Peter King. 2010. Fizzling the Plutonium Economy: Origins of the April 1977 Carter Administration Fuel Cycle Policy Transition. Master's thesis, Harvard University, Extension School. Citable link https://nrs.harvard.edu/URN-3:HUL.INSTREPOS:37367548 Terms of Use This article was downloaded from Harvard University’s DASH repository, and is made available under the terms and conditions applicable to Other Posted Material, as set forth at http:// nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of- use#LAA Fizzling the Plutonium Economy: Origins of the April 1977 Carter Administration Fuel Cycle Policy Transition Peter Williams A Thesis in the Field of History for the Degree of Master of Liberal Arts in Extension Studies Harvard University May 2010 © 2010 Peter Williams Abstract This study examines the scientific advocacy that shaped President Carter’s April 1977 policy decision to block the domestic implementation of so-called “plutonium economy” technologies, and thereby mandate the use of an “open” or “once–through” fuel cycle for U.S. nuclear power reactors. This policy transition was controversial, causing friction with U.S. allies, with the nuclear power industry, and with Congress. Early in his presidential campaign, Carter criticized the excessive federal financial commitment to developing plutonium-based reactors and adopted the view that the weapons proliferation risks of plutonium economy technologies were serious and needed to be addressed. -
National States and International Science: a Comparative History of International Science Congresses in Hitler's Germany, Stalin's Russia, and Cold War United States
National States and International Science: A Comparative History of International Science Congresses in Hitler's Germany, Stalin's Russia, and Cold War United States Osiris 2005 Doel, Ronald E. Department of History (and Department of Geosciences), Oregon State University Originally published by: The University of Chicago Press on behalf of The History of Science Society and can be found at: http://www.jstor.org/action/showPublication?journalCode=osiris Citation: Doel, R. E. (2005). National states and international science; A comparative history of international science congresses in Hitler's Germany, Stalin's Russia, and Cold War United States. Osiris, 20, 49-76. Available from JSTOR website: http://www.jstor.org/stable/3655251 National States and International Science: A ComparativeHistory of International Science Congresses in Hitler's Germany, Stalin's Russia, and Cold WarUnited States Ronald E. Doel, Dieter Hoffmann, and Nikolai Krementsov* ABSTRACT Priorstudies of modem scientificinternationalism have been writtenprimarily from the point of view of scientists, with little regardto the influenceof the state. This studyexamines the state'srole in internationalscientific relations. States sometimes encouragedscientific internationalism;in the mid-twentiethcentury, they often sought to restrictit. The presentstudy examines state involvementin international scientific congresses, the primaryintersection between the national and interna- tional dimensionsof scientists'activities. Here we examine three comparativein- stancesin which such -
A Correlation of Cytological and Genetical Crossing-Over in Zea Mays. PNAS 17:492–497
A CORRELATION OF CYTOLOGICAL AND GENETICAL CROSSING-OVER IN ZEA MAYS HARRIET B. CREIGHTON BARBARA MCCLINTOCK Botany Department Cornell University Ithaca, New York Creighton, H., and McClintock, B. 1931 A correlation of cytological and genetical crossing-over in Zea mays. PNAS 17:492–497. E S P Electronic Scholarly Publishing http://www.esp.org Electronic Scholarly Publishing Project Foundations Series –– Classical Genetics Series Editor: Robert J. Robbins The ESP Foundations of Classical Genetics project has received support from the ELSI component of the United States Department of Energy Human Genome Project. ESP also welcomes help from volunteers and collaborators, who recommend works for publication, provide access to original materials, and assist with technical and production work. If you are interested in volunteering, or are otherwise interested in the project, contact the series editor: [email protected]. Bibliographical Note This ESP edition, first electronically published in 2003 and subsequently revised in 2018, is a newly typeset, unabridged version, based on the 1931 edition published by The National Academy of Sciences. Unless explicitly noted, all footnotes and endnotes are as they appeared in the original work. Some of the graphics have been redone for this electronic version. Production Credits Scanning of originals: ESP staff OCRing of originals: ESP staff Typesetting: ESP staff Proofreading/Copyediting: ESP staff Graphics work: ESP staff Copyfitting/Final production: ESP staff © 2003, 2018 Electronic Scholarly Publishing Project http://www.esp.org This electronic edition is made freely available for educational or scholarly purposes, provided that this copyright notice is included. The manuscript may not be reprinted or redistributed for commercial purposes without permission. -
Meeting Review: Bioinformatics and Medicine – from Molecules To
Comparative and Functional Genomics Comp Funct Genom 2002; 3: 270–276. Published online 9 May 2002 in Wiley InterScience (www.interscience.wiley.com). DOI: 10.1002/cfg.178 Feature Meeting Review: Bioinformatics And Medicine – From molecules to humans, virtual and real Hinxton Hall Conference Centre, Genome Campus, Hinxton, Cambridge, UK – April 5th–7th Roslin Russell* MRC UK HGMP Resource Centre, Genome Campus, Hinxton, Cambridge CB10 1SB, UK *Correspondence to: Abstract MRC UK HGMP Resource Centre, Genome Campus, The Industrialization Workshop Series aims to promote and discuss integration, automa- Hinxton, Cambridge CB10 1SB, tion, simulation, quality, availability and standards in the high-throughput life sciences. UK. The main issues addressed being the transformation of bioinformatics and bioinformatics- based drug design into a robust discipline in industry, the government, research institutes and academia. The latest workshop emphasized the influence of the post-genomic era on medicine and healthcare with reference to advanced biological systems modeling and simulation, protein structure research, protein-protein interactions, metabolism and physiology. Speakers included Michael Ashburner, Kenneth Buetow, Francois Cambien, Cyrus Chothia, Jean Garnier, Francois Iris, Matthias Mann, Maya Natarajan, Peter Murray-Rust, Richard Mushlin, Barry Robson, David Rubin, Kosta Steliou, John Todd, Janet Thornton, Pim van der Eijk, Michael Vieth and Richard Ward. Copyright # 2002 John Wiley & Sons, Ltd. Received: 22 April 2002 Keywords: bioinformatics; -
Theodosius Dobzhansky: a Man for All Seasons
GENERAL ARTICLE Theodosius Dobzhansky: A Man For All Seasons Francisco J Ayala In 1972, Theodosius Dobzhansky addressed the convention of Francisco J Ayala the National Association of Biology Teachers on the theme obtained his Ph D with Theodosius Dobzhansky "Nothing in biology makes sense except in the light of evolu in the 1960s and is tion". The title of that address (published in The American presently the Donald Bren Biology Teacher, Vol. 35, pp. 125-129) might serve as an epigram Professor of Biological of Dobzhansky's worldview and life, although it is limited in Sciences at the University of California, Irvine and a scope, for Dobzhansky believed and propounded that the impli member of President cations of biological evolution reach much beyond biology into Clinton's Committee of philosophy, sociology, and even socio-political issues. The Advisors on Science and place of biological evolution in human thought was, according Technology. He is a member of the U S to Dobzhansky, best expressed in a passage that he often quoted National Academy of from Pierre Teilhard de Chardin: "(Evolution) is a general Sciences and has been postulate to which all theories, all hypotheses, all systems must President and Chairman hence forward bow and which they must satisfy in order to be of the Board of the American Association for thinkable and true. Evolution is a light which illuminates all the Advancement of facts, a trajectory which all lines of thought must follow - this is Science. He has worked what evolution is". extensively on the population ecology and The Modern Synthesis of Evolutionary Theory evolutionary genetics of Drosophila species. -
Medical Advisory Board September 1, 2006–August 31, 2007
hoWard hughes medical iNstitute 2007 annual report What’s Next h o W ard hughes medical i 4000 oNes Bridge road chevy chase, marylaNd 20815-6789 www.hhmi.org N stitute 2007 a nn ual report What’s Next Letter from the president 2 The primary purpose and objective of the conversation: wiLLiam r. Lummis 6 Howard Hughes Medical Institute shall be the promotion of human knowledge within the CREDITS thiNkiNg field of the basic sciences (principally the field of like medical research and education) and the a scieNtist 8 effective application thereof for the benefit of mankind. Page 1 Page 25 Page 43 Page 50 seeiNg Illustration by Riccardo Vecchio Südhof: Paul Fetters; Fuchs: Janelia Farm lab: © Photography Neurotoxin (Brunger & Chapman): Page 3 Matthew Septimus; SCNT images: by Brad Feinknopf; First level of Rongsheng Jin and Axel Brunger; iN Bruce Weller Blake Porch and Chris Vargas/HHMI lab building: © Photography by Shadlen: Paul Fetters; Mouse Page 6 Page 26 Brad Feinknopf (Tsai): Li-Huei Tsai; Zoghbi: Agapito NeW Illustration by Riccardo Vecchio Arabidopsis: Laboratory of Joanne Page 44 Sanchez/Baylor College 14 Page 8 Chory; Chory: Courtesy of Salk Janelia Farm guest housing: © Jeff Page 51 Ways Illustration by Riccardo Vecchio Institute Goldberg/Esto; Dudman: Matthew Szostak: Mark Wilson; Evans: Fred Page 10 Page 27 Septimus; Lee: Oliver Wien; Greaves/PR Newswire, © HHMI; Mello: Erika Larsen; Hannon: Zack Rosenthal: Paul Fetters; Students: Leonardo: Paul Fetters; Riddiford: Steitz: Harold Shapiro; Lefkowitz: capacity Seckler/AP, © HHMI; Lowe: Zack Paul Fetters; Map: Reprinted by Paul Fetters; Truman: Paul Fetters Stewart Waller/PR Newswire, Seckler/AP, © HHMI permission from Macmillan Page 46 © HHMI for Page 12 Publishers, Ltd.: Nature vol. -
Introduction and Historical Perspective
Chapter 1 Introduction and Historical Perspective “ Nothing in biology makes sense except in the light of evolution. ” modified by the developmental history of the organism, Theodosius Dobzhansky its physiology – from cellular to systems levels – and by the social and physical environment. Finally, behaviors are shaped through evolutionary forces of natural selection OVERVIEW that optimize survival and reproduction ( Figure 1.1 ). Truly, the study of behavior provides us with a window through Behavioral genetics aims to understand the genetic which we can view much of biology. mechanisms that enable the nervous system to direct Understanding behaviors requires a multidisciplinary appropriate interactions between organisms and their perspective, with regulation of gene expression at its core. social and physical environments. Early scientific The emerging field of behavioral genetics is still taking explorations of animal behavior defined the fields shape and its boundaries are still being defined. Behavioral of experimental psychology and classical ethology. genetics has evolved through the merger of experimental Behavioral genetics has emerged as an interdisciplin- psychology and classical ethology with evolutionary biol- ary science at the interface of experimental psychology, ogy and genetics, and also incorporates aspects of neuro- classical ethology, genetics, and neuroscience. This science ( Figure 1.2 ). To gain a perspective on the current chapter provides a brief overview of the emergence of definition of this field, it is helpful -
Mapping Our Genes—Genome Projects: How Big? How Fast?
Mapping Our Genes—Genome Projects: How Big? How Fast? April 1988 NTIS order #PB88-212402 Recommended Citation: U.S. Congress, Office of Technology Assessment, Mapping Our Genes-The Genmne Projects.’ How Big, How Fast? OTA-BA-373 (Washington, DC: U.S. Government Printing Office, April 1988). Library of Congress Catalog Card Number 87-619898 For sale by the Superintendent of Documents U.S. Government Printing Office, Washington, DC 20402-9325 (order form can be found in the back of this report) Foreword For the past 2 years, scientific and technical journals in biology and medicine have extensively covered a debate about whether and how to determine the function and order of human genes on human chromosomes and when to determine the sequence of molecular building blocks that comprise DNA in those chromosomes. In 1987, these issues rose to become part of the public agenda. The debate involves science, technol- ogy, and politics. Congress is responsible for ‘(writing the rules” of what various Federal agencies do and for funding their work. This report surveys the points made so far in the debate, focusing on those that most directly influence the policy options facing the U.S. Congress, The House Committee on Energy and Commerce requested that OTA undertake the project. The House Committee on Science, Space, and Technology, the Senate Com- mittee on Labor and Human Resources, and the Senate Committee on Energy and Natu- ral Resources also asked OTA to address specific points of concern to them. Congres- sional interest focused on several issues: ● how to assess the rationales for conducting human genome projects, ● how to fund human genome projects (at what level and through which mech- anisms), ● how to coordinate the scientific and technical programs of the several Federal agencies and private interests already supporting various genome projects, and ● how to strike a balance regarding the impact of genome projects on international scientific cooperation and international economic competition in biotechnology. -
Barbara Mcclintock
Barbara McClintock Lee B. Kass and Paul Chomet Abstract Barbara McClintock, pioneering plant geneticist and winner of the Nobel Prize in Physiology or Medicine in 1983, is best known for her discovery of transposable genetic elements in corn. This chapter provides an overview of many of her key findings, some of which have been outlined and described elsewhere. We also provide a new look at McClintock’s early contributions, based on our readings of her primary publications and documents found in archives. We expect the reader will gain insight and appreciation for Barbara McClintock’s unique perspective, elegant experiments and unprecedented scientific achievements. 1 Introduction This chapter is focused on the scientific contributions of Barbara McClintock, pioneering plant geneticist and winner of the Nobel Prize in Physiology or Medicine in 1983 for her discovery of transposable genetic elements in corn. Her enlightening experiments and discoveries have been outlined and described in a number of papers and books, so it is not the aim of this report to detail each step in her scientific career and personal life but rather highlight many of her key findings, then refer the reader to the original reports and more detailed reviews. We hope the reader will gain insight and appreciation for Barbara McClintock’s unique perspective, elegant experiments and unprecedented scientific achievements. Barbara McClintock (1902–1992) was born in Hartford Connecticut and raised in Brooklyn, New York (Keller 1983). She received her undergraduate and graduate education at the New York State College of Agriculture at Cornell University. In 1923, McClintock was awarded the B.S.