A History of Genetics
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Models of the Gene Must Inform Data-Mining Strategies in Genomics
entropy Review Models of the Gene Must Inform Data-Mining Strategies in Genomics Łukasz Huminiecki Department of Molecular Biology, Institute of Genetics and Animal Biotechnology, Polish Academy of Sciences, 00-901 Warsaw, Poland; [email protected] Received: 13 July 2020; Accepted: 22 August 2020; Published: 27 August 2020 Abstract: The gene is a fundamental concept of genetics, which emerged with the Mendelian paradigm of heredity at the beginning of the 20th century. However, the concept has since diversified. Somewhat different narratives and models of the gene developed in several sub-disciplines of genetics, that is in classical genetics, population genetics, molecular genetics, genomics, and, recently, also, in systems genetics. Here, I ask how the diversity of the concept impacts data-integration and data-mining strategies for bioinformatics, genomics, statistical genetics, and data science. I also consider theoretical background of the concept of the gene in the ideas of empiricism and experimentalism, as well as reductionist and anti-reductionist narratives on the concept. Finally, a few strategies of analysis from published examples of data-mining projects are discussed. Moreover, the examples are re-interpreted in the light of the theoretical material. I argue that the choice of an optimal level of abstraction for the gene is vital for a successful genome analysis. Keywords: gene concept; scientific method; experimentalism; reductionism; anti-reductionism; data-mining 1. Introduction The gene is one of the most fundamental concepts in genetics (It is as important to biology, as the atom is to physics or the molecule to chemistry.). The concept was born with the Mendelian paradigm of heredity, and fundamentally influenced genetics over 150 years [1]. -
The Early History of Medical Genetics in Canada William Leeming OCAD University [email protected]
OCAD University Open Research Repository Faculty of Liberal Arts & Sciences and School of Interdisciplinary Studies 2004 The Early History of Medical Genetics in Canada William Leeming OCAD University [email protected] © Oxford University Press. This is the author's version of the work. It is posted here for your personal use. Not for redistribution. Original source at DOI: 10.1093/shm/17.3.481. Recommended citation: Leeming, W. “The Early History of Medical Genetics in Canada.” Social History of Medicine 17.3 (2004): 481–500. Web. Leeming, W. (2004). The early history of medical genetics in Canada. Social History of Medicine, 17(3), 481-500. Pre-Publication Draft The Early History of Medical Genetics in Canada Abstract: This article shows that the intellectual and specialist movements that supported the growth of medical genetics in Canada between 1947 and 1990 were emergent phenomena, created, split, and reattached to different groups of actors, and reconfigured numerous times over the course of four decades. In each instance, new kinds of working relationships appeared; sets of diverse actors in local university- hospital settings coalesced into a new collectivity; and, as a collectivity, actors defined and/or redefined occupational roles and work rules. In its beginnings, medical genetics appears to be the object of a serious institutional manoeuver: a movement in support of the creation of examining and teaching positions in human genetics in North American medical schools. With time, the institutionalization of ‘medical genetics’ took hold, spurred on by changes in the rate and direction of service delivery associated with genetic consultation and laboratory services in clinical settings. -
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. -
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 -
Barbara Mcclintock's World
Barbara McClintock’s World Timeline adapted from Dolan DNA Learning Center exhibition 1902-1908 Barbara McClintock is born in Hartford, Connecticut, the third of four children of Sarah and Thomas Henry McClintock, a physician. She spends periods of her childhood in Massachusetts with her paternal aunt and uncle. Barbara at about age five. This prim and proper picture betrays the fact that she was, in fact, a self-reliant tomboy. Barbara’s individualism and self-sufficiency was apparent even in infancy. When Barbara was four months old, her parents changed her birth name, Eleanor, which they considered too delicate and feminine for such a rugged child. In grade school, Barbara persuaded her mother to have matching bloomers (shorts) made for her dresses – so she could more easily join her brother Tom in tree climbing, baseball, volleyball, My father tells me that at the and football. age of five I asked for a set of tools. He My mother used to did not get me the tools that you get for an adult; he put a pillow on the floor and give got me tools that would fit in my hands, and I didn’t me one toy and just leave me there. think they were adequate. Though I didn’t want to tell She said I didn’t cry, didn’t call for him that, they were not the tools I wanted. I wanted anything. real tools not tools for children. 1908-1918 McClintock’s family moves to Brooklyn in 1908, where she attends elementary and secondary school. In 1918, she graduates one semester early from Erasmus Hall High School in Brooklyn. -
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. -
Elements of Genetics
GENETICS AND PLANT BREEDING Elements of Genetics Dr. B. M. Prasanna National Fellow Division of Genetics Indian Agricultural Research Institute New Delhi-110012 (12-06- 2007) CONTENTS Introduction History Cell Cell Division Special Chromosomes Dominance Relationships Gene Interactions Multiple Alleles Sex Determination Sex Linkage Linkage and Crossing Over Genetic Mapping Structural Changes in Chromosomes Numerical Changes in Chromosomes Nature of the Genetic Material Gene Regulation Operon Concept Gene Concept Mutation Polygenic and Quantitative Inheritance Extrachromosomal Inheritance Plant Tissue Culture Keywords Mitosis, Meiosis 1 Introduction In biology, heredity is the passing on of characteristics from one generation to the next. It is the reason why offspring look like their parents. It also explains why cats always give birth to kittens and never puppies. The process of heredity occurs among all living organisms, including animals, plants, bacteria, protists and fungi. Genetic variation refers to the variation in a population or species. Genetics is the study of heredity and variation in living organisms. Two research approaches were historically important in helping investigators understand the biological basis of heredity. The first of these approaches, ‘transmission genetics’, involved crossing organisms and studying the offsprings' traits to develop hypotheses about the mechanisms of inheritance. The second approach involved using cytological techniques to study the machinery and processes of cellular reproduction. This approach laid a solid foundation for the more conceptual understanding of inheritance that developed as a result of transmission genetics. Ever since 1970s, with the advent of molecular tools and techniques, geneticists are able to intensively analyze genetic basis of trait variation in various organisms, including plants, animals and humans. -
Chromosomal Theory and Genetic Linkage
362 Chapter 13 | Modern Understandings of Inheritance 13.1 | Chromosomal Theory and Genetic Linkage By the end of this section, you will be able to do the following: • Discuss Sutton’s Chromosomal Theory of Inheritance • Describe genetic linkage • Explain the process of homologous recombination, or crossing over • Describe chromosome creation • Calculate the distances between three genes on a chromosome using a three-point test cross Long before scientists visualized chromosomes under a microscope, the father of modern genetics, Gregor Mendel, began studying heredity in 1843. With improved microscopic techniques during the late 1800s, cell biologists could stain and visualize subcellular structures with dyes and observe their actions during cell division and meiosis. With each mitotic division, chromosomes replicated, condensed from an amorphous (no constant shape) nuclear mass into distinct X-shaped bodies (pairs of identical sister chromatids), and migrated to separate cellular poles. Chromosomal Theory of Inheritance The speculation that chromosomes might be the key to understanding heredity led several scientists to examine Mendel’s publications and reevaluate his model in terms of chromosome behavior during mitosis and meiosis. In 1902, Theodor Boveri observed that proper sea urchin embryonic development does not occur unless chromosomes are present. That same year, Walter Sutton observed chromosome separation into daughter cells during meiosis (Figure 13.2). Together, these observations led to the Chromosomal Theory of Inheritance, which identified chromosomes as the genetic material responsible for Mendelian inheritance. Figure 13.2 (a) Walter Sutton and (b) Theodor Boveri developed the Chromosomal Theory of Inheritance, which states that chromosomes carry the unit of heredity (genes). -
Epigenetics Is Normal Science, but Don't Call It Lamarckian
Extended Abstract Volume 6:3, 2020 DOI: 6.2472/imedipce.2020.6.002 Journal of Clinical Epigenetics ISSN: 2472-1158 Open Access Epigenetics is Normal Science, But Don’t Call It Lamarckian David Penny New Zealand Extended Abstract they are general (but not necessarily universal) because they are found in Excavates, which many people consider are ancestral to other eukaryotes [6, 7]. Similarly, an important point is that Epigenetic mechanisms are increasingly being accepted as an integral methylation, phosphorylation, etc. of the DNA and of the histones is a part of normal science. Earlier genetic studies appear to have part of normal evolution (at least in eukaryotes that have the assumed that the only changes were ‘mutations’ as a result of a nucleosome structure) [8]. One of the most interesting aspects is change in the DNA sequence. If any such changes altered the amino methylation (and hydroxymethylation) of cytosine, and this is found in acid sequences then it was effectively a mutation, and if it occurred in many deep branching eukaryotes [9]. Typically there is methylation of a germline cell (including in unicellular organisms) then it could be cytosine molecules, especially in CpG (cytosine followed by guanine) passed on to subsequent generations. However, it is increasingly regions. The role of small RNAs in helping regulate the levels of apparent that other changes are also important, for example, changes protein expression is discussed in [10]. The main point here is that to methylation patterns, and to the histone proteins. Epigenetics was protein expression levels are very variable in all cells – it is not just sometimes consider ‘additional’ to classical genetics, but it is still fully classical genetics that is important; there are many epigenetic dependent on DNA, RNA and protein sequences, and at least since [1] mechanisms affecting the differences in protein expression. -
Using Classical Genetics Simulator (CGS) to Teach Students the Basics of Genetic Research
Tested Studies for Laboratory Teaching Proceedings of the Association for Biology Laboratory Education Vol. 33, 85–94, 2012 Using Classical Genetics Simulator (CGS) to Teach Students the Basics of Genetic Research Jean Heitz1, Mark Wolansky2, and Ben Adamczyk3 1University of Wisconsin, Zoology Department, 250 N. Mills Street, Madison WI 53706 USA 2University of Alberta, Department of Biological Science, Edmonton AB, CAN T6G 2E9 3Genedata, MA, A-1 Cranberry HI, Lexington MA 02421 USA ([email protected];[email protected];[email protected]) Some experiments are not well suited to large introductory labs because of space, time and funding constraints. Among these are classical Mendelian genetics investigations. Cyber labs can overcome these constraints. Classi- cal Genetics Simulator (CGS) gives students the opportunity to perform controlled crosses with model organisms much like a geneticist would do. CGS provides populations of Drosophila, Arabidopsis or mice with unknown patterns of inheritance and gives students the tools to design and perform experiments to discover these patterns. Students require an understanding of the what, why and how of solving genetic problems to successfully complete our cyber genetics lab activities. Keywords: Mendelian genetics, simulator, classical genetics simulator (CGS), linkage, monohybrid, dihybrid Introduction In large introductory biology classes some labs are dif- How can students get practice doing what geneticists ficult to do because of space, time and funding constraints. actually do? Among these are classical Mendelian genetics investiga- An obvious way for students to get practice doing what tions. As a result, we have turned to cyber labs. Working geneticists do is to conduct actual crosses. -
Alfred Henry Sturtevant (1891–1970) [1]
Published on The Embryo Project Encyclopedia (https://embryo.asu.edu) Alfred Henry Sturtevant (1891–1970) [1] By: Gleason, Kevin Keywords: Thomas Hunt Morgan [2] Drosophila [3] Alfred Henry Sturtevant studied heredity in fruit flies in the US throughout the twentieth century. From 1910 to 1928, Sturtevant worked in Thomas Hunt Morgan’s research lab in New York City, New York. Sturtevant, Morgan, and other researchers established that chromosomes play a role in the inheritance of traits. In 1913, as an undergraduate, Sturtevant created one of the earliest genetic maps of a fruit fly chromosome, which showed the relative positions of genes [4] along the chromosome. At the California Institute of Technology [5] in Pasadena, California, he later created one of the firstf ate maps [6], which tracks embryonic cells throughout their development into an adult organism. Sturtevant’s contributions helped scientists explain genetic and cellular processes that affect early organismal development. Sturtevant was born 21 November 1891 in Jacksonville, Illinois, to Harriet Evelyn Morse and Alfred Henry Sturtevant. Sturtevant was the youngest of six children. During Sturtevant’s early childhood, his father taught mathematics at Illinois College in Jacksonville. However, his father left that job to pursue farming, eventually relocating seven-year-old Sturtevant and his family to Mobile, Alabama. In Mobile, Sturtevant attended a single room schoolhouse until he entered a public high school. In 1908, Sturtevant entered Columbia University [7] in New York City, New York. As a sophomore, Sturtevant took an introductory biology course taught by Morgan, who was researching how organisms transfer observable characteristics, such as eye color, to their offspring. -
A Brief History of Genetics
A Brief History of Genetics A Brief History of Genetics By Chris Rider A Brief History of Genetics By Chris Rider This book first published 2020 Cambridge Scholars Publishing Lady Stephenson Library, Newcastle upon Tyne, NE6 2PA, UK British Library Cataloguing in Publication Data A catalogue record for this book is available from the British Library Copyright © 2020 by Chris Rider All rights for this book reserved. No part of this book may be reproduced, stored in a retrieval system, or transmitted, in any form or by any means, electronic, mechanical, photocopying, recording or otherwise, without the prior permission of the copyright owner. ISBN (10): 1-5275-5885-1 ISBN (13): 978-1-5275-5885-4 Cover A cartoon of the double-stranded helix structure of DNA overlies the sequence of the gene encoding the A protein chain of human haemoglobin. Top left is a portrait of Gregor Mendel, the founding father of genetics, and bottom right is a portrait of Thomas Hunt Morgan, the first winner of a Nobel Prize for genetics. To my wife for her many years of love, support, patience and sound advice TABLE OF CONTENTS List of Figures.......................................................................................... viii List of Text Boxes and Tables .................................................................... x Foreword .................................................................................................. xi Acknowledgements ................................................................................. xiii Chapter 1 ...................................................................................................