CRI - Teaching Through Research - John Jungck - BioQuest
1. INTERDISCIPLINARY QUANTITATIVE
REASONING IN BIOLOGY EDUCATION
26 March 2014
John R. Jungck
BioQUEST Curriculum Consortium
Editor, Biology International, International Union of Biological Sciences
Professor of Biological & Mathematical Sciences, University of Delaware, USA
Director, Interdisciplinary Sciences Learning Laboratories
jungck@udel.edu <http://bioquest.org>
16. What happens when?
• Your ruler doesn’t
seem to work right?
• Your mean and
variance don’t
agree with another
published study?
• Duplicates of
experiments vary
widely?
17. Fractal Measurements
• Rulers
• Box Plots
• Concentric Annuli
• Log-Log Plots
Fractal Dimension Calculator
Written by Paul Bourke (February 2003)
18. • Bacterial colonies exhibit complex growth patterns on starvation
conditions (Shane Stafford and Yan Li:):!
• Experimentally:!
• The growth pattern and fractal dimension depend on both the
nutrient concentration and roughness of the agar substrate !
• Bacteria perform a random walk like movement on the substrate,
within a well-defined envelope (lubrication layer)!
• Under extreme adverse living conditions, patterns become dense
again by chemo tactic signaling!
E Ben-Jacob et al, Nature,368, (47)1994,!
Fractal Bacterial Growth
23. Dangers of Linear Transformations:!
Michaelis-Menten Enzyme kinetics!
-d[S]/dt = Vmax[S]/KM + [S]!
24. Computational Complexity
EBI: “Important: We kindly ask all users of EMBL-EBI Web Services to submit tool jobs in batches of up
to 25 at a time and to not submit more until the results and processing has completed for these. This enables
users as well as the service maintainers to deal more easily with local and remote network outages as well as
scheduled or unscheduled downtime.”
28. Barbara Maria Stafford!
!
!
“What is lacking today, however, is a concomitant!
high-level visual education to accompany the!
advances in visualization”!
!
!
!
Artful Science: Enlightenment, Entertainment and the!
Eclipse of Visual Education, MIT Press (1994)!
29. Hans Rosling and Gapminder:
provide resources for context
www.gapminder.org
30. Gapminder: Goal to make data
accessible and understandable
• What’s here: Gapminder WORLD from
UNICEF
35. BIRDD:
Species with regard to Wing Length
Upper Beak Length and Beak Height
http://people.eku.edu/ritchisong/
RITCHISO//DarwinsFinches.jpg
Evolution class yesterday: Jared Wynne, David Meltzer, and Aaron Nesser
38. Scaling and
shear
transformations
capture beak
shape variation
in Darwin’s
finches.
O. Camp , R.
Mallarinob, A.
Herrelb, A.
Abzhanovb, and
M. P. Brennera/
School of
Engineering and
Applied
Sciences,
Harvard
University
and Department
of Organismic
and Evolutionary
Biology, Harvard
University
48. SequenceIt!
COMBINATORIAL EXPLOSION
19! = 1.22 * 1017
opportunity for “infinite opportunity” to
do research
heuristics vs. algorithms
realism: run out of material; improperly
designed experiments = poor results
49. Mastermind
Mastermind Mathematics:
Logic, Strategies, and Proofs
by Mathew Mitchell.
Key Curriculum Press.
Mathematics teachers have long used the game MASTERMIND to
teach logic and deduction. Mathew Mitchell, an associate
professor at the University of San Francisco Department of
Learning and Instruction, makes the connections between
game strategies and mathematics concepts such as problem-
solving and proof strategies. As students use this book and
play MASTERMIND, apply strategies such as establishing
subgoals, making a chart, deductive reasoning, eliminating
possibilities, pattern searching, and proof by contradiction.
http://www.maa.org/mathland/mathtrek_10_11_99.html
Ivars Peterson’s Math Trek column on math & “Mastermind.”
50.
51. Done by an undergraduate
Alfred Henry Sturtevant 1891-1970
First Ever Genetic Map - Drosophila X-chromosome!
3!
53. Benzer 1959, 1961 papers:
topology and topography of
genetic fine structure
• Topography paper:
– map several thousand point mutations using nested set of deletion alleles
– note difference between spontaneous and induced mutations, first detailed analysis of
mutagen specificity
54. javaBENZER Problem Solving Tools:
Solve Problem = rearranges Shkurba (Mut) into Shkurba form
with all Maximal Cliques ordered on main diagonal
Applications: Protein and Nucleic Acid Sequencing;
Restriction, Deletion, and Complementation Mapping;
Microarray Gene Expression Data; Food Webs
My interactive solution
Computer algorithm solution
Lower right to upper left is isomorphic to upper left to lower right
55.
56. Phylogenetic Trees
Fitch, W.M. and Margoliash, E. 1967. The construction of phylogenetic trees - a
generally applicable method utilizing estimates of the mutation distance
obtained from cytochrome c sequences. Science 155: 279-284.
Walter M. Fitch Emmanuel Margoliash
4!
59. An example problem using
Phylogenetic Analysis
• 1990: HIV+ dentist in Florida
• several patients also HIV+
• was the dentist the source?
• some patients with other HIV risk
factors
• virus from dentist, patients, others
• evolutionary relationships of virus gp120
gene → transmission of virus
4!
61. Split Decomposition:
Evaluate Evidence for Internal Branches
Alpha !AAGAAGCAGGGGCTGGAGATGAAGGCCCATG!
Beta !AAGAAGCGGAGGCTGGAGCTGAAGGCCCATG!
Gamma !AAGAAGCGGAGGGTGGAGCTGAAGGCCCACG!
Delta !GAGAAGAGGAGCCTGGAGCTGAAGGCCCACA!
Three possible unrooted trees:
A
B
G
D
A
G
B
D
A
D
B
G
67. Nobel Prize 1969
Salvador Luria Max Delbrück
1924-1998 1919-2004
“Fluctuation Test” Poisson Statistics Mutation Rates!
Darwin vs Lamarck!
Considered by many as the finest experiment in 20th Century!
9!
72. E. O. Wilson
Robert MacArthur
Island
Biogeography
Theory
Allometry
Species-Area-
Distance-Law
8!
Source of most CONSEVATION
strategies and policies!
74. “Bacterial genetic diversity in this system increased with increasing island size according to the familiar
species-area power law (Fig. 1A). The slope z of the relationship (z = 0.26) is indistinguishable from published
values for larger organisms (Fig. 1B). The data show that area size strongly influences the diversity of these
microbial communities.” (Bell et al. 2005 Science 308:1884).
Spatial scaling of bacteria in water-filled treeholes
75. Lee Segel Prize for Best Paper 2010
Brynja R. Kohler, Rebecca J. Swank, James W.
Haefner, James A. Powell.
"Leading Students to Investigate Diffusion as a Model
of Brine Shrimp Movement”
Bull. Math. Biol. 72: 230-57 (2010).
Society for Mathematical Biology
