In Pursuit of the Gene
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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]. -
Jazz and the Cultural Transformation of America in the 1920S
Louisiana State University LSU Digital Commons LSU Doctoral Dissertations Graduate School 2003 Jazz and the cultural transformation of America in the 1920s Courtney Patterson Carney Louisiana State University and Agricultural and Mechanical College, [email protected] Follow this and additional works at: https://digitalcommons.lsu.edu/gradschool_dissertations Part of the History Commons Recommended Citation Carney, Courtney Patterson, "Jazz and the cultural transformation of America in the 1920s" (2003). LSU Doctoral Dissertations. 176. https://digitalcommons.lsu.edu/gradschool_dissertations/176 This Dissertation is brought to you for free and open access by the Graduate School at LSU Digital Commons. It has been accepted for inclusion in LSU Doctoral Dissertations by an authorized graduate school editor of LSU Digital Commons. For more information, please [email protected]. JAZZ AND THE CULTURAL TRANSFORMATION OF AMERICA IN THE 1920S A Dissertation Submitted to the Graduate Faculty of the Louisiana State University and Agricultural and Mechanical College in partial fulfillment of the requirements for the degree of Doctor of Philosophy in The Department of History by Courtney Patterson Carney B.A., Baylor University, 1996 M.A., Louisiana State University, 1998 December 2003 For Big ii ACKNOWLEDGEMENTS The real truth about it is no one gets it right The real truth about it is we’re all supposed to try1 Over the course of the last few years I have been in contact with a long list of people, many of whom have had some impact on this dissertation. At the University of Chicago, Deborah Gillaspie and Ray Gadke helped immensely by guiding me through the Chicago Jazz Archive. -
Use of Genomic Tools to Discover the Cause of Champagne Dilution Coat Color in Horses and to Map the Genetic Cause of Extreme Lordosis in American Saddlebred Horses
University of Kentucky UKnowledge Theses and Dissertations--Veterinary Science Veterinary Science 2014 USE OF GENOMIC TOOLS TO DISCOVER THE CAUSE OF CHAMPAGNE DILUTION COAT COLOR IN HORSES AND TO MAP THE GENETIC CAUSE OF EXTREME LORDOSIS IN AMERICAN SADDLEBRED HORSES Deborah G. Cook University of Kentucky, [email protected] Right click to open a feedback form in a new tab to let us know how this document benefits ou.y Recommended Citation Cook, Deborah G., "USE OF GENOMIC TOOLS TO DISCOVER THE CAUSE OF CHAMPAGNE DILUTION COAT COLOR IN HORSES AND TO MAP THE GENETIC CAUSE OF EXTREME LORDOSIS IN AMERICAN SADDLEBRED HORSES" (2014). Theses and Dissertations--Veterinary Science. 15. https://uknowledge.uky.edu/gluck_etds/15 This Doctoral Dissertation is brought to you for free and open access by the Veterinary Science at UKnowledge. It has been accepted for inclusion in Theses and Dissertations--Veterinary Science by an authorized administrator of UKnowledge. For more information, please contact [email protected]. STUDENT AGREEMENT: I represent that my thesis or dissertation and abstract are my original work. Proper attribution has been given to all outside sources. I understand that I am solely responsible for obtaining any needed copyright permissions. I have obtained needed written permission statement(s) from the owner(s) of each third-party copyrighted matter to be included in my work, allowing electronic distribution (if such use is not permitted by the fair use doctrine) which will be submitted to UKnowledge as Additional File. I hereby grant to The University of Kentucky and its agents the irrevocable, non-exclusive, and royalty-free license to archive and make accessible my work in whole or in part in all forms of media, now or hereafter known. -
The Runners of Shawnee Road
University of New Orleans ScholarWorks@UNO University of New Orleans Theses and Dissertations Dissertations and Theses Fall 12-20-2013 The Runners of Shawnee Road Melissa Remark University of New Orleans, [email protected] Follow this and additional works at: https://scholarworks.uno.edu/td Part of the Fiction Commons Recommended Citation Remark, Melissa, "The Runners of Shawnee Road" (2013). University of New Orleans Theses and Dissertations. 1761. https://scholarworks.uno.edu/td/1761 This Thesis is protected by copyright and/or related rights. It has been brought to you by ScholarWorks@UNO with permission from the rights-holder(s). You are free to use this Thesis in any way that is permitted by the copyright and related rights legislation that applies to your use. For other uses you need to obtain permission from the rights- holder(s) directly, unless additional rights are indicated by a Creative Commons license in the record and/or on the work itself. This Thesis has been accepted for inclusion in University of New Orleans Theses and Dissertations by an authorized administrator of ScholarWorks@UNO. For more information, please contact [email protected]. The Runners of Shawnee Road A Thesis Submitted to the Graduate Faculty of The University of New Orleans in partial fulfillment of the requirements for the degree of Master of Fine Arts in Film, Theater and Communication Arts Creative Writing by Melissa Remark B.A. Trent University, 2010 Diploma, Humber College, 2000 December, 2013 The Sheeny Man rides through the streets pulling his wagon of junk. Sometimes he is black, sometimes he is white, and sometimes he is French. -
Assortative Mating (4 P.)
Evolutionary Dynamics: Population Genetics and Ecological Models WS 2019/2020 course number: MA4453-KP05 Assignment 1 due: October 28 Mendel's experiments & Punnett squares (4 P.) In the lecture, we discussed Mendel's experiments with garden peas in which he considered one character (e.g. ower color or seed shape). In a second step, he considered two characters simultaneously. He started with two pure lines. One had yellow (dominant allele Y ), wrinkled (recessive allele r) seeds. The other had green (recessive allele y), round (dominant allele R) seeds. I.e. the genotypes of these pure lines were Y Y rr and yyRR. He crossed these two lines to obtain the F1 generation. He then obtained the F2 generation through selng of individuals from the F1 generation. Draw the corresponding Punnett square to determine the genotypes and phenotypes that are generated in this way. What are the proportions of the observed phenotypes if you determine proportions by counting the respective cells in the Punnett square? Mendel indeed observed these proportions. However, in 1905, William Bateson, Edith Re- becca Saunders, and Reginald Punnett performed a similar experiment in sweet pea plants. They simultaneously considered ower color and pollen shape and found dierent proportions than Mendel. How can this discrepancy be explained? You can read Mendel's original publication here (in German!): http: // www. deutschestextarchiv. de/ book/ view/ mendel_ pflanzenhybriden_ 1866? p= 14 Assortative mating (4 P.) In the lecture, we studied randomly mating individuals. However, in reality, mating is often non-random. E.g. individuals may prefer to mate with individuals that are similar to them with respect to some trait. -
The Population Problem Inherited Evolutio
2000 Earthlearningidea - http://www.earthlearningidea.com/ top edge of Sorting out the evolution of evolution headlines page Lay out your own timeline of how the theory of evolution developed Cut off the left hand edge of these four Earthlearningidea sheets and stick them together to form a timeline. Then stick it down on a bench or table. The ‘Evolution of evolution’ timeline Cut out the milestone boxes in the evolution of evolutionary theory below into strips. Leave the dates attached for less able pupils, but remove them for the more able. Then invite the pupils to sort out the headlines 1975 and place them in the correct places on the timeline – to show how evolutionary theory Photo: Chris King evolved. Species static This image is in the public The early part of the bible is interpreted to show that domain because species are static and there is no evolution. The date of its copyright has expired. 1650 creation of all species is calculated by Archbishop Ussher as 4004BC. Archbishop Ussher Evolution – but how? This image is in the public Early evolutionary ideas are presented by natural domain because 1740 philosophers, Pierre Maupertuis and Erasmus Darwin. its copyright has - expired. 1796 1950 Pierre Maupertuis The population problem This image is in the public Thomas Malthus publishes his idea that populations domain because increase geometrically (2,4,16) whilst food production its copyright has 1798 only increases arithmetically (2,3,4) so there must be expired. population crashes. Thomas Malthus Inherited evolution Permission is granted to copy, Jean-Baptiste Lamarck develops his evolutionary theory distribute and/or – that evolution occurs because offspring change in modify this document under 1800 response to the environment, and these changes are the terms of the inherited from their parents (later shown to be 1925 GNU Free incorrect). -
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. -
Contestations, Conflicts and Music-Power: Mevlevi Sufism in the 21St Century Turkey
CONTESTATIONS, CONFLICTS AND MUSIC-POWER: MEVLEVI SUFISM IN THE 21ST CENTURY TURKEY A THESIS SUBMITTED TO THE GRADUATE SCHOOL OF SOCIAL SCIENCES OF MIDDLE EAST TECHNICAL UNIVERSITY BY NEVİN ŞAHİN IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY IN THE DEPARTMENT OF SOCIOLOGY FEBRUARY 2016 Approval of the Graduate School of Social Sciences _____________________________ Prof. Dr. Meliha Altunışık Director I certify that this thesis satisfies all the requirements as a thesis for the degree of Doctor of Philosophy. _____________________________ Prof. Dr. Sibel Kalaycıoğlu Head of Department This is to certify that we have read this thesis and that in our opinion it is fully adequate, in scope and quality, as a thesis for the degree of Doctor of Philosophy. _____________________________ Assoc. Prof. Dr. Mustafa Şen Supervisor Examining Committee Members Assoc. Prof. Dr. Zana Çıtak (METU, IR) _____________________________ Assoc. Prof. Dr. Mustafa Şen (METU, SOC) _____________________________ Assoc. Prof. Dr. Cenk Güray (YBU, MUS) _____________________________ Assist. Prof. Dr. Yelda Özen (YBU, SOC) _____________________________ Assist. Prof. Dr. Çağatay Topal (METU, SOC) _____________________________ I hereby declare that all information in this document has been obtained and presented in accordance with academic rules and ethical conduct. I also declare that, as required by these rules and conduct, I have fully cited and referenced all material and results that are not original to this work. Name, Last name: Nevin Şahin Signature: iii ABSTRACT CONTESTATIONS, CONFLICTS AND MUSIC-POWER: MEVLEVI SUFISM IN THE 21ST CENTURY TURKEY Şahin, Nevin PhD. Department of Sociology Supervisor: Assoc. Prof. Dr. Mustafa Şen February 2016, 232 pages Established as a Sufi order in central Anatolia following the death of Rumi, Mevlevi Sufism has influenced the spirituality of people for over 8 centuries. -
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. -
The Punnett Square Was Created in the Early 1900S by Reginald Punnett
Punnett Square The Punnett Square was created in the early 1900s by Reginald Punnett. Punnett was born in 1875 and was the eldest of three children. He grew up in England and was fascinated by the natural sciences at an early age. When he was young, he was often stricken by appendix issues and had to stay quiet during recovery. During one particular recovery period, he spent a large amount of time reading his father’s library on natural history, which sparked his interest and had a lasting impact on his career choices (Crew 1967). As Punnett continued his love for science, he eventually became one of the first scientists to study genetics at Cambridge University and helped to establish the field there. He spent a significant amount of time conducting genetics research with the leading scientists of his day, including William Bateson and G. H. Hardy (Cold Spring Harbor Laboratory 2011). Together they were strong proponents of the genetic work of Gregor Mendel, who today is credited as the father of genetics. In 1905, Punnett devised what is known today as the Punnett Square (Arizona State University 2012). The Punnett Square is used to illustrate some of Mendel’s discoveries including the segregation of DNA into different gametes upon gamete formation. The Punnett Square was designed as a teaching tool and is still used in classrooms today. The premise is simple; the genetic contribution of the two individuals under study is listed on each side of the square. For example, we are to cross two sweet pea individuals that have the genotypes Gg and gg. -
Genome As a Multipurpose Structure Built by Evolution Michel Morange
1 Genome as a multipurpose structure built by evolution Michel Morange, Centre Cavaillès, République des savoirs USR 3608, Ecole normale supérieure, 29 rue d’Ulm, 75230 Paris Cedex05, France Email: [email protected] Abstract The publication in 2012 of the results of the ENCODE program generated an acrimonious debate about the role of junk DNA. This debate is a symptom of the difficulties of dovetailing functional and evolutionary descriptions of genomes. My argument is that extant genomes are the result of a progressive evolutionary construction. To the basic function – to give rise to RNA and proteins – have been successively added other functions – regulation by microRNA and epigenetic marks, for instance. This process of complexification was not a regular one, but the result of a complex evolutionary history, different for the different genomes. Better knowledge of the evolutionary history of genomes would help to understand these structures and their functions. Historians and philosophers of biology have amply discussed the difficulty, even the impossibility, of providing a precise definition of a gene (Beurton et al. 2000). The genome no longer appears as a collection of similar genes, but as a multitasking structure formed of different types of genetic elements (Gingeras 2006). Participants in these debates nonetheless often agree on one issue, that the genome is (and has to be) something well defined: a collection of genes, a 2 reservoir of junk DNA, or a structure filled with regulatory sequences. My point of view will be different: the genome is what evolution has progressively made of it. This vision has three important consequences. -
STORIA DEL PENSIERO BIOLOGICO EVOLUTIVO Con Riflessioni Di Filosofia Ambientale
STORIA DEL PENSIERO BIOLOGICO EVOLUTIVO con riflessioni di filosofia ambientale STORIA DEL PENSIERO BIOLOGICO EVOLUTIVO con riflessioni di filosofia ambientale Piergiacomo Pagano 2013 ENEA Agenzia nazionale per le nuove tecnologie, l’energia e lo sviluppo economico sostenibile Lungotevere Thaon di Revel, 76 00196 ROMA ISBN 978-88-8286-288-6 Foto in copertina In alto: fotografie di Fabio Conte Sfondo e riquadro: fotografie di Piergiacomo Pagano (Pellicani a Hervey Bay, Queensland, Australia, novembre 2003; Baobab, mousse du Senegal, febbraio 1991) STORIA DEL PENSIERO BIOLOGICO EVOLUTIVO con riflessioni di filosofia ambientale PIERGIACOMO PAGANO P. Pagano, Storia del Pensiero Biologico Evolutivo, ENEA INDICE Premessa …………………………………………………………………………………………..… 11 Introduzione ………………………………………………………………………………………… 13 1 Sui tre inspiegabili fatti che misero in dubbio la Creazione ……………………………………... 17 1.1 In antichità: cause finali e progetto …………………………………………………………...……... 17 1.2 L’età moderna ……………………………………………………………………………………...... 18 1.3 La grande diversità degli animali e delle piante …………………………………………………….. 19 1.4 Le palesi ingiustizie ……………………………………………………………………...………….. 20 1.5 La presenza di fossili inglobati nelle rocce ………………………………………………………..... 21 2 La Natura, gli organismi e la loro classificazione ……………………………………………...… 23 2.1 La classificazione in Platone …………………………………………………………………...…… 23 2.2 Classificazioni …………………………………………………………………………………...….. 25 2.3 Dopo Platone ………………………………………………………………………………………... 25 2.4 Aristotele e lo studio della Natura