cri - teaching through research - john jungck - bioquest
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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
[email protected] <http://bioquest.org>
Examples: Population Size
(Capture-Mark-Recapture) Buffer Preparation
(Henderson-Hasselbach) Serial Dilution
(Enumerating Bacteria) Allele Frequencies (Classroom Data)
Modeling More Mold
Measuring the area covered by mold over intervals of time!
Image J Measurement
“Exponential growth and then levels off” - Microbio Teacher!
Robert Blystone Trinity University
Ka-me: A Voronoi Image Analyzer
Bioinformatics (2012)
Problem for today: How do we understand biological tessella7ons that are produced by several rounds of successive cell division?
Richard Jones
Mito7c Division 2
Abstract!
Bibliography!
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?
Fractal Measurements • Rulers
• Box Plots • Concentric Annuli
• Log-Log Plots
Fractal Dimension Calculator Written by Paul Bourke (February 2003)
• 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
Fractal Dimension of Healthy and Leukemic Cells
Dangers of Linear Transformations:!Michaelis-Menten Enzyme kinetics!
-d[S]/dt = Vmax[S]/KM + [S]!
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.”
Visualization
visualization + equations + simulations lead to better understanding
aesthetic aspects attract attention examples: WWW, images, toys, gadgets
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) !
Hans Rosling and Gapminder: provide resources for context
www.gapminder.org
Gapminder: Goal to make data accessible and understandable
• What’s here: Gapminder WORLD from UNICEF
Health vs Wealth
Visualizing Data
www.gapminder.org/
Starvation Plot
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
Arthur Nature Reviews Genetics; 11 April 2006
Bioorthogonal Transformations!
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
D’Arcy Wentworth Thompson: Linear
D’Arcy Wentworth Thompson: Affine
D’Arcy Wentworth Thompson: Quadratic
STEM TO STEAM
http://www.steamedu.com/!!
Richard Dawkins & Lalla Ward (“Dr. Who”)
(1994)!
Seeing is:
• Doing • Measuring • Testing hypotheses • Re-visioning • Modeling
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
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.”
Done by an undergraduate
Alfred Henry Sturtevant 1891-1970
First Ever Genetic Map - Drosophila X-chromosome !
3!
Linkage Analysis in the
Biological ESTEEM Project Excel Simulations and Tools for
Exploratory, Experiential Mathematics
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
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
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!
4!
Graph Theory: Phylogenetic Trees!4!
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!
CDC Conclusion Dentist Patient Patient Patient Other Other Other
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
Alpha !AAGAAGCAGGGGCTGGAGATGAAGGCCCATG!Beta !AAGAAGCGGAGGCTGGAGCTGAAGGCCCATG!Gamma !AAGAAGCGGAGGGTGGAGCTGAAGGCCCACG!Delta !GAGAAGAGGAGCCTGGAGCTGAAGGCCCACA!
A
B
G
D
dAB dGD
dAG
dBD
dcentral =
dcentral
2 ONLY for the correct tree!!!
How can we calculate the length of the central branch?
dAB
dGD
dAG + dBD - ( dAB + dGD )
Split Decomposition
Which tree topology is most consistent with the data?
The Algorithmic Beauty of Sea Shells
Biological Cellular Automata Laboratory (BioCA Lab)
Author(s): John Jungck, University of Delaware Jennifer Spangenberg, Washington State University
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!
FLUCTUATION TEST
A TEST OF DARWINISM VS LAMARCKISM
Genetics Construction Kit Gene Interaction
1:2:1:2:4:2:1:2:1 3:6:3:1:2:1 9:3:3:1 Epistasis
9:3:4 9:7 15:1 13:3 12:3:1 Polygenes
1:4:6:4:1 Quasi-quantitative
10:5:1 11:4:1 11:2:2:1
Genetics Construction Kit (the integrated organismal model)
Linkage (Haldane Function) Multiple Loci/ Stochasticity 1-10 Multiple Alleles 1-5 Sex-linkage, Sex-limited, Sex-influenced Gene Interaction/Polygenes/Epistasis Monoecious/Dioecious Lethality/Penetrance/Pleiotropy
3!
Beer-Lambert law,
E. O. Wilson
Robert MacArthur
Island Biogeography
Theory
Allometry Species-Area- Distance-Law
8!
Source of most CONSEVATION strategies and policies!
Island Biogeography: Species-Area Law!
“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
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
Invade the Biology Lab!
SMB Lee Segel Prize