Statistics for Learning Genetics Abigail Sheena Charles Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy under the Executive Committee of the Graduate School of Arts and Sciences COLUMBIA UNIVERSITY 2012 © 2012 Abigail Sheena Charles All rights reserved ABSTRACT Statistics for Learning Genetics Abigail Sheena Charles This study investigated the knowledge and skills that biology students may need to help them understand statistics/mathematics as it applies to genetics. The data are based on analyses of current representative genetics texts, practicing genetics professors‘ perspectives, and more directly, students‘ perceptions of, and performance in, doing statistically-based genetics problems. This issue is at the emerging edge of modern college-level genetics instruction, and this study attempts to identify key theoretical components for creating a specialized biological statistics curriculum. The goal of this curriculum will be to prepare biology students with the skills for assimilating quantitatively-based genetic processes, increasingly at the forefront of modern genetics. To fulfill this, two college level classes at two universities were surveyed. One university was located in the northeastern US and the other in the West Indies. There was a sample size of 42 students and a supplementary interview was administered to a select 9 students. Interviews were also administered to professors in the field in order to gain insight into the teaching of statistics in genetics. Key findings indicated that students had very little to no background in statistics (55%). Although students did perform well on exams with 60% of the population receiving an A or B grade, 77% of them did not offer good explanations on a probability question associated with the normal distribution provided in the survey. The scope and presentation of the applicable statistics/mathematics in some of the most used textbooks in genetics teaching, as well as genetics syllabi used by instructors do not help the issue. It was found that the text books, often times, either did not give effective explanations for students, or completely left out certain topics. The omission of certain statistical/mathematical oriented topics was seen to be also true with the genetics syllabi reviewed for this study. Nonetheless, although the necessity for infusing these quantitative subjects with genetics and, overall, the biological sciences is growing (topics including synthetic biology, molecular systems biology and phylogenetics) there remains little time in the semester to be dedicated to the consolidation of learning and understanding. TABLE OF CONTENTS TABLE OF CONTENTS ................................................................................................................. i LIST OF TABLES ......................................................................................................................... iv LIST OF FIGURES ........................................................................................................................ v DEDICATION ............................................................................................................................... vi ACKNOWLEDGEMENTS .......................................................................................................... vii CHAPTER I .................................................................................................................................... 1 Introduction ..................................................................................................................................... 1 Need for Study ........................................................................................................................ 1 Purpose of Study ..................................................................................................................... 4 Overview of Procedures .......................................................................................................... 4 CHAPTER II ................................................................................................................................... 6 Literature Review............................................................................................................................ 6 The Status of the Content Domain .............................................................................................. 7 The Relationships of Learning Resources, Teachers and Students .......................................... 13 A Rationale for Curriculum Design in Mathematically-based Genetics .................................. 24 A Review of the Current Political Agenda that Promotes Statistical Education ...................... 29 Details of the Types of Statistical Genetics Tools and Applications that Call for an ............... 36 In-depth Statistical Understanding. ........................................................................................... 36 Documentation from Professionals in Industry ........................................................................ 38 CHAPTER III ............................................................................................................................... 40 Methods......................................................................................................................................... 40 Study Setting.............................................................................................................................. 40 Population ................................................................................................................................. 40 Description of Participant Sample........................................................................................ 40 Data Gathering Procedures ....................................................................................................... 42 Recruitment of Participants .................................................................................................. 42 Sequence of the Study in Overview: ...................................................................................... 43 Data Analyses ........................................................................................................................... 46 Methods Applied for Each Research Question ..................................................................... 46 Analysis Tools .......................................................................................................................... 49 Statistical Tests ......................................................................................................................... 49 i CHAPTER IV ............................................................................................................................... 50 Results ........................................................................................................................................... 50 Research Question 1 ................................................................................................................. 50 A Note on Epigenetics ........................................................................................................... 60 Research Question 2 ................................................................................................................. 61 Textbook Analysis ................................................................................................................. 62 Results from Student Survey.................................................................................................. 77 Research Question 3 ................................................................................................................. 83 Results from the Survey Administered to Students at the Beginning and End of the Semester ............................................................................................................................................... 83 Results from Student Interviews ............................................................................................ 91 Research Question 4 ................................................................................................................. 94 Results from Survey at the End of the Semester .................................................................... 98 CHAPTER V .............................................................................................................................. 109 Discussion ................................................................................................................................... 109 More Time for Probability in Genetics Courses ..................................................................... 109 Statistics Class for Biology Students ...................................................................................... 109 Genetics Textbooks Lack of Explanation of Probability Content .......................................... 110 Teaching Statistics as it Pertains to Genetics Subject Matter ................................................. 110 Introducing Statistics Early in a Student‘s Career .................................................................. 111 Computing in Genetics Courses.............................................................................................. 111 Developing Areas in Genetics ................................................................................................ 111 CHAPTER VI ............................................................................................................................. 121 Summary, Conclusions and Recommendations .......................................................................... 121 Summary and Conclusions ..................................................................................................... 121 Recommendations for Future Research .................................................................................. 124 REFERENCES ........................................................................................................................... 127 APPENDICES ............................................................................................................................ 131 APPENDIX A ......................................................................................................................... 131 Survey Questionnaires ............................................................................................................ 131 APPENDIX B ......................................................................................................................... 138 Expanded Results Tables ........................................................................................................ 138 APPENDIX C ......................................................................................................................... 174 Definitions and Further Explanations ..................................................................................... 174 APPENDIX D ......................................................................................................................... 220 ii IRB Forms ............................................................................................................................... 220 APPENDIX E ......................................................................................................................... 227 Genetics Syllabi ...................................................................................................................... 227 iii LIST OF TABLES Table 1: Teaching, Learning and Learning Tools Synergy .......................................................... 24 Table 2: Interest Level .................................................................................................................. 41 Table 3: Type of Matriculation: Postbac/Other or Regular .......................................................... 41 Table 4: Age by Gender ................................................................................................................ 42 Table 5: Principles of Genetics by Snustad & Simmons .............................................................. 63 Table 6: Genetics: Analysis and Principles by Brooker ............................................................... 65 Table 7: Genetics: A Conceptual Approach by B.A. Pierce ......................................................... 67 Table 8: Introduction to Genetics Analysis by Griffiths, Wessler, Lewontin, Gelbart, Suzuki, Miller............................................................................................................................................. 71 Table 9: Genetics: From Genes to Genomes by Hartwell, Hood, Goldberg, Reynolds, Silver and Veres ............................................................................................................................................. 73 Table 10: Mendelian Genetics Explanation Rating by Having Studied Mendelian Genetic or Not ....................................................................................................................................................... 78 Table 11: Linkage Answer Rating by Linkage Analysis Response .............................................. 80 Table 12: Punnett Square Explanation Rating by Punnett Square Response ............................... 81 Table 13: Normal Probability Distribution Familiarity by Explanation Rating ........................... 84 Table 14: Chi Square Explanation by Familiar with the Chi Square Test Rating ........................ 87 Table 15: Chi Square Explanation by Know How to Use the Probabilities of Chi Square Dist. Rating ............................................................................................................................................ 88 Table 16: Biology Class with Statistics Content........................................................................... 89 Table 17: Number of Statistics Classes Taken ............................................................................. 90 Table 18: Number of Statistical Tests/Methods Identified ........................................................... 90 Table 19: Interest Type by Punnett Square Explanation Rating ................................................... 91 Table 20: Student Interview Matrix .............................................................................................. 93 Table 21: Interview Results with Professors ................................................................................ 96 Table 22: Statistics Class for Biology Students ............................................................................ 98 Table 23: Difficulty Level of Statistics Questions ........................................................................ 99 Table 24: Computer Programming Class .................................................................................... 102 Table 25: Familiarity with Relational Database ......................................................................... 102 Table 26: Student Final Grade .................................................................................................... 106 Table 27: Student Final Grade by Normal Probability Explanation Rating ............................... 108 Table B10: Interest Type by Chi Square Explanation Rating..................................................... 151 iv LIST OF FIGURES Figure 1: DNA Microarray Analysis Example ............................................................................. 12 Figure 2: The Complementary Triadic Relationship Between Three Components of a Coherent Learning Experience or Curriculum Design. ................................................................................ 13 Figure 3: Transcribe and Translate a Gene ................................................................................... 21 Figure 4: The Three Cases of Similarity ....................................................................................... 55 Figure 5: Outgroup Comparison ................................................................................................... 56 Figure 6: Genetics Distance Map ................................................................................................. 58 Figure 7: HHM and Phylo-HHM Example ................................................................................ 119 Figure C3: Heterogeneous nuclear RNA (hnRNA) .................................................................... 185 Figure C8: The Phenotypes of Two Independent Traits Show a 9:3:3:1 Ratio in the F2 generation ..................................................................................................................................................... 196 v DEDICATION To my grandparents Ralph and Floris Slinger vi