|
|
|
Fall 2007, Weds 3-5:30pm, CERIA 125 Castetter 258
Topics in Interdisciplinary Biology and Biological Sciences (TIBBS)
(Enroll for credit in the following depts: CS/591C 004,
Stat/579D 004, Math/579D 004, Anthro 560, Bio 503 004)
This course presents and discusses recent work in biological science that bridges scientific disciplines, integrates different approaches, and demonstrates the effectiveness of collaborative research. The multiple units in this course will be from Biology, Math and Statistics, Computer Sciences and Electrical and Computer Engineering. (class flyer)
UNIT 1: Anthropogenic climate shiftsfrom both modern and paleoperspectives
 Biology:
Felisa Smith
With Marcy Litvak & Will Pockman
Over the past few decades perceptible changes in a number of temperature and climatic measures have occurred on every continent. A recent meta analysis has elegantly demonstrated that over 50% of species already demonstrate a response. Yet the changes that have already occurred (~1°C over the past 50 years) will be dwarfed by what is expected over the next century (up to 5.8°C). Better predictions of how organisms will respond to climatic fluctuations are urgently needed. Studies have documented the entire gamut of changes possible, including tolerance, local extirpation and range shifts, as well as adaptive changes in genetics and/or morphology. In this unit we will explore the current thought about the evolutionary capability of organisms, using both modern and paleoperspectives. This unit will explore studies conducted at a variety of temporal, spatial and heirarchical levels, which provide an integrated perspective into how organisms may respond to ongoing anthropogenic climate shifts.
Assignments
Student presentations and student led discussion
Guidelines: These will occur in the 3rd and 4th week of class (Sept 5, 12).
Working with 2-3 students from other departments, you will research and prepare a short powerpoint presentation on one of the issues below or another that I have approved. Be sure in your presentation to clearly state the issue(s) and outline the debate, (if relevant) present arguments and analysis, and provide your integrated interpretation. Prepare these as if you were talking to an informed technical audience, but one drawn largely from outside the disciplines represented by your topic. Your group will initate and guide a discussion on this topic, so you might consider preparing leading questions to facilitate the discussion. Presentations should be no longer than ~10-12 minutes, with an additional ~10 minutes set aside for the discussion.
Suggested Topics:
- Climate projections: what assumptions go into the proposed climate simulation models that lead to different predictions about the trajectory of climate change? Which are more realistic?
- China and global warming: how will the world’s largest country solve their energy needs and how might this influence the rate of anthropogenic warming?
- Climate and the past: the collapse of Easter island and other pre-industrial anthropogenic disasters. What does this suggest about sustainability?
- Climate mitigation: how are we going to get around? Can biofuels provide a viable alternative to fossil fuels?
- Climate mitigation: can local actions by citizens, towns and states effectively reduce global emissions?
- Climate “fixes”: deep ocean carbon disposal, iron fertilization & other (sometimes wacky) proposals.
- Climate and society: what climate changes and impacts can we expect in our neck of the woods (the western US)?
- Climate and human health: how might anthropogenic climate change influence disease dynamics and prevalance?
Readings:
Week 1
- Human Domination of Earth's Ecosystems (.pdf)
Peter M. Vitousek; Harold A. Mooney; Jane Lubchenco; Jerry M. Melillo. Science, New Series, Vol. 277, No. 5325. (Jul. 25, 1997), pp. 494-499
- Intergovernmental Panel on Climate Change (website)
Fourth Assesment Report
- Working Group I (summary) (reports)
- Working Group II (summary) (reports)
- Working Group III (summary) (reports)
Week 2
- Genetic consequences of climatic oscillations in the Quaternary (.pdf)
G.M. Hewitt; Philosphical Transactions of the Royal Society of London, 359, 183-195 (2004)
- Evolutionary Response to Climatic Change? (.pdf)
B. Huntley; Heredity, 98, 247-248 (2007)
- A globally coherent fingerprint of climate change impacts across natural systems (.pdf)
Camille Parmesan & Gary Yohe; Nature, 421, 37-42 (2003)
UNIT 2: Numb3rs in the real world: Integrating mathematics and biology to understand and predict infectious
disease dynamics
 Math/Stats & Biology: Helen Wearing
Taking influenza as a case study we will consider how mathematical models are being used to help explain patterns of disease spread and evolution, as well as investigate control measures for future outbreaks. The unit will be a mixture of lectures, discussion and a small student group project. (click here for unit web page updated by Dr. Wearing )
Pre-Unit
Click
here to take a very short survey about math & programming
experience Thanks!
B.A. Wilcox & R.R. Colwell. Emerging and reemerging
infectious diseases: biocomplexity as an
interdisciplinary paradigm. EcoHealth 2: 244-257 (2005). (.pdf
)
Week 1
Background
D.J.D. Earn, J. Dushoff & S.A. Levin. Ecology and evolution of the flu. Trends in
Ecology & Evolution 17: 334-340 (2002). (.pdf)
Discussion papers (to be read
before Week 2)
S.S. Morse. Pandemic influenza: Studying the lessons of
history. (Commentary) PNAS 104: 7582-7587 (2007). (.pdf)
R.J. Hatchett, C.E. Mecher & M. Lipsitch. Public
health interventions and epidemic intensity during the
1918 influenza pandemic. PNAS 104: 7582-7587 (2007). (.pdf)
M.C.J. Bootsma & N.M. Ferguson. The effect of public
health measures on the 1918 influenza pandemic in
U.S. cities. PNAS 104: 7588-7593 (2007). (.pdf)
Week 2
Background Nature's 1918 influenza pandemic web focus
Discussion papers (to be read
before Week 3)
C. Viboud, O.N. Bjornstad, D.L. Smith, L. Simonsen,
M.A. Miller & B.T. Grenfell. Synchrony, waves and spatial hierarchies in
the spread of influenza. Science 312: 7582-7587 (2006). (.pdf)
J.S. Brownstein, C.J. Wolfe & K.D. Mandl. Empirical
evidence for the effect of airline travel on
inter-regional influenza spread in the United
States. PLoS Medicine 33: e401 (2006). (.pdf)
UNIT 3: Functional Imaging of the Brain
 Electrical and Computer Engineering: Vince Calhoun
In these lectures we will cover basic functional magnetic resonance imaging acquisition, preprocessing, basic analysis, and advanced analysis. Example of applications will be provided throughout and hopefully we will be able to arrange a tour of the MRI scanner.
Week 1
Readings
- fMRI Primer: Doug Noll (.pdf)
- Imaging Cognitive Anatomy: Karl Friston (.pdf)
- Effective Paradigm Design: Donaldson & Buckner (.pdf)
Take a look at the fMRI course at Duke, has some great slides for learning fMRI
Week 2
Reading
- Functional MRI (.pdf)
- Functional MRI Intro PowerPoint Slides(.pdf)
Remember we are meeting at The Mind Institute on October 31st at 3:00 pm, Directions
UNIT 4: Theory of Animal Motion and Spread of Epidemics
 Physics and Astronomy: Nitant Kenkre
Description of the motion of animals such as rodents, and of the transmission of infection of epidemics based on such motion will be taught in this unit. Examples of epidemics are the Hantavirus, the West Nile virus and the Plague. A physicist's perspective on these interdisciplinary problems will be explained and tools taught from the ground up. Spatiotemporal patterns in bacteria in a Petri dish, refugia of epidemics in a landscape, and patterns arising from nonlinear competitive interactions will be among the subjects discussed.
Syllabus
- How biologists and physicists can collaborate: two channels of cooperation
- Emphasis on motion: of fronts, of rodents, of bacteria
- Background on the Hantavirus and the West Nile Virus
- Basics of the description of motion: random walks and diffusion equations
- Home ranges of animals and Smoluchowski equations
- Methods of nonlinear science: ecology and the Fisher equation
- Variants of the Fisher equation
- Bacteria in a Petri dish, experimental verification pattern formation
- Allee effect in ecology and consequences on population dynamics
- Predator effects, juvenile- adult interaction and miscellanea
- Cooperative motion of birds, fish and other animals: flocks and schools
Readings
G. Abramson, V. M. Kenkre: Spatio- Temporal Patterns in Hantavirus
Infection, Phys. Rev.
E 66, 011912, 1- 5 (2002). (.pdf)
M.A. Aguirre, G. Abramson, A.R. Bishop, V.M. Kenkre: Simulations in
the Mathematical
Modeling of the Spread of the Hantavirus, Phys. Rev. E 66, 041908
(2002). (.pdf)
V. M. Kenkre: Memory functions, Nonlinear Techniques, and Kinetic
Equation
Approaches. In: V. M. Kenkre and K. Lindenberg (eds). “Modern
Challenges in Statistical
Mechanics: Patterns, Growth, and the Interplay of Nonlinearity and
CoConference Proceedings Volume 658 (ISBN 0- 7354- 0118- 7) (2003). (.pdf)
G. Abramson, V. M. Kenkre, T. L. Yates, and R. Parmenter: Traveling
Waves of Infection in the Hantavirus, Bull. Math. Biology (2003) 65, 519-534. (.pdf)
V. M. Kenkre and M. Kuperman: Applicability of the Fisher equation to bacterial population dynamics, Phys. Rev. E 67, 051921 (2003). (.pdf)
L. Giuggioli and V. M. Kenkre: Analytic Solutions of a Nonlinear
Convective Equation in Population Dynamics, Physica D
183/3- 4, 245- 259 (2003). (.pdf)
M. A. Fuentes, M. N. Kuperman, and V.M. Kenkre: Nonlocal Interaction Effects on Pattern Formation
in Population Dynamic, Phys. Rev. Lett. 91, 158104- 1 (2003). (.pdf)
M. A. Fuentes, M. Kuperman, and V. M. Kenkre: Analytical
Considerations in the Study of
Spatial Patterns Arising from Nonlocal Interaction Effects in Population Dynamics, J. Phys.
Chem. B 108, 10505- 10508 (2004). (.pdf)
M. Ballard, V. M. Kenkre, and M. N. Kuperman: Periodically Varying
Externally Imposed
Environmental Effects on Population Dynamics, Phys. Rev. E 70, 031912
(2004). (.pdf)
V. M. Kenkre: Results from Variants of the Fisher Equation in the Study of Epidemics and Bacteria, Physica A 342, 242- 248 (2004). (.pdf)
V. M. Kenkre, R. R. Parmenter, I. D. Peixoto, and L. Sadasiv: A Theoretical Framework for the Analysis of the West Nile Virus Epidemic, Mathematical and Computer Modelling 42, 313- 324 (2005). (.pdf)
L. Giuggioli, G. Abramson, V.M. Kenkre, G. Suzan, E. Marcé, T. Yates: Diffusion and Home Range Parameters from Rodent Population Measurements in Panama, Bulletin of Mathematical Biology 67, 1135- 1149 (2005). (.pdf)
V. M. Kenkre, Statistical Mechanical Considerations in the Theory of the Spread of Hantavirus, Physica A, 356, 121- 126 (2005). (.pdf)
M. G. Clerc, D. Escaff, and V. M. Kenkre: Patterns and Localized Structures in Population Dynamics, Phys. Rev. E 72, 056217 (2005). (.pdf)
I. Peixoto, L. Giuggioli, and V.M. Kenkre: Arbitrary Nonlinearities in Convective Population Dynamics with Small Diffusion, Phys. Rev. E 72, 041902 (2005). (.pdf)
G. Abramson, L. Giuggioli, V.M. Kenkre, J. Dragoo, B. Parmenter, C. Parmenter, T. Yates: Diffusion and Home Range Parameters of Rodents II: Peromyscus Maniculatus in New Mexico, Ecological Complexity 3, 64- 70 (2006). (.pdf)
L. Giuggioli, G. Abramson, V.M. Kenkre, C. Parmenter, T. Yates: Theory of Home Range Estimation from Displacement Measurements of Animal Populations, J. Theoretical Biology 240, 126- 135, (2006). (.pdf)
V. M. Kenkre, L. Giuggioli, G. Abramson, and G. Camelo- Neto, Theory of Hantavirus Infection Spread incorporating Localized Adult and Itinerant Juvenile Mice, Eur. Phys. J. B 55, 461- 470 (2007). (.pdf)
L. Giuggioli, G.M. Viswanathan, V.M. Kenkre, R.R. Parmenter, and T.L. Yates: Effects of Finite Probing Windows on the Interpretation of the Multifractal Property of Random Walks, Europhysics Letters 77, 40004- p1- 5 (2007). (.pdf)
|
|
