Statistics for Learning Genetics Abigail Sheena Charles Submitted

247 Pages·2012·5.65 MB·English

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
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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

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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

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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

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DEDICATION

To my grandparents

Ralph and Floris Slinger

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