
Quantitative Biosciences
Description
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A hands-on approach to quantitative reasoning in the life sciences Quantitative Biosciences establishes the quantitative principles of how living systems work across scales, drawing on classic and modern discoveries to present a case study approach that links mechanisms, models, and measurements. Each case study is organized around a central question in the life sciences: Are mutations dependent on selection? How do cells respond to fluctuating signals in the environment? How do organisms move in flocks given local sensing? How does the size of an epidemic depend on its initial speed of spread? Each question provides the basis for introducing landmark advances in the life sciences while teaching students-whether from the life sciences, physics, computational sciences, engineering, or mathematics-how to reason quantitatively about living systems given uncertainty.
- Draws on real-world case studies in molecular and cellular biosciences, organismal behavior and physiology, and populations and ecological communities
- Stand-alone lab guides available in Python, R, and MATLAB help students move from learning in the classroom to doing research in practice
- Homework exercises build on the lab guides, emphasizing computational model development and analysis rather than pencil-and-paper derivations
- Suitable for capstone undergraduate classes, foundational graduate classes, or as part of interdisciplinary courses for students from quantitative backgrounds
- Can be used as part of conventional, flipped, or hybrid instruction formats
- Additional materials available to instructors, including lesson plans and homework solutions
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Content
- Cover
- Contents
- Preface
- Quantitative Biosciences at All Scales of Life
- The Goal
- The Structure of this Book
- You Can Do It
- Acknowledgments
- I. Molecular and Cellular Biosciences
- 1. Fluctuations and the Nature of Mutations
- 1.1. Chance Favors the Independent Mutation
- 1.2. Cellular Phenotypes
- 1.3. Mutations that Depend on Selection
- 1.4. Independent Mutations: A Continuous Model
- 1.5. Modeling the Growth of (Discrete) Mutants
- 1.6. Variance of Mutants When Mutations are Independent of Selection
- 1.7. On (In)Direct Inference
- 1.8. Take-Home Messages
- 1.9. Homework Problems
- 1.10. Technical Appendix
- 2. Bistability of Genetic Circuits
- 2.1. More is Different
- 2.2. Molecular Cast and Scene
- 2.3. The First Ingredient: Regulation of a Target Gene
- 2.4. Feedback and Bistability-Autoregulation
- 2.5. The Dynamics of a Genetic Toggle Switch
- 2.6. Take-Home Messages
- 2.7. Homework Problems
- 2.8. Technical Appendix
- 3. Stochastic Gene Expression and Cellular Variability
- 3.1. Living with Randomness
- 3.2. Stochasticity in Gene Regulation
- 3.3. Characterizing Dynamics of Individual Cells, Given Stochastic Gene Expression
- 3.4. Is Gene Expression Bursty?
- 3.5. The Geometry of Bursts
- 3.6. Take-Home Messages
- 3.7. Homework Problems
- 3.8. Technical Appendix
- 4. Evolutionary Dynamics: Mutations, Selection, and Diversity
- 4.1. Evolution in Action
- 4.2. Selection and the Disappearance of Diversity
- 4.3. Mechanisms that Restore Diversity
- 4.4. Stochasticity in the Evolution of Populations-Baseline Expectations
- 4.5. Evolutionary Dynamics with Stochasticity and Selection
- 4.6. Sweeps or Hitchhiking or Both?
- 4.7. Take-Home Messages
- 4.8. Homework Problems
- 4.9. Technical Appendix
- II. Organismal Behavior and Physiology
- 5. Robust Sensing and Chemotaxis
- 5.1. On Taxis
- 5.2. Why Swim?
- 5.3. The Behavior of Swimming E. coli
- 5.4. Chemotaxis Machinery
- 5.5. Signaling Cascades
- 5.6. Fine-Tuned Adaptation
- 5.7. Buffering and Robust Cellular Adaptation
- 5.8. Take-Home Messages
- 5.9. Homework Problems
- 5.10. Technical Appendix
- 6. Nonlinear Dynamics and Signal Processing in Neurons
- 6.1. Walking in the Path of Hodgkin and Huxley
- 6.2. The Brain: Memory, Learning, and Behavior
- 6.3. Of Ions and Neurons
- 6.4. Dynamical Properties of Excitable Neuronal Systems
- 6.5. From Neurons to Neural Networks and Information Processing
- 6.6. Take-Home Messages
- 6.7. Homework Problems
- 6.8. Technical Appendix
- Color Plates
- 7. Excitations and Signaling from Cells to Tissue
- 7.1. From Excitable Cells to Excitable Systems
- 7.2. Principles of Oscillatory Dynamics
- 7.3. Relaxation Oscillations-a Generalized View
- 7.4. Principles of Excitability: From Cardiac Cells to Tissue
- 7.5. Take-Home Messages
- 7.6. Homework Problems
- 7.7. Technical Appendix
- 8. Organismal Locomotion through Water, Air, and Earth
- 8.1. Movement from Within
- 8.2. Movement with Brief Moments in Air
- 8.3. Principles of Slow Swimming
- 8.4. Terrestrial Locomotion
- 8.5. Take-Home Messages
- 8.6. Homework Problems
- 8.7. Technical Appendix
- III. Populations and Ecological Communities
- 9. Flocking and Collective Behavior: When Many Become One
- 9.1. Life is with Other Organisms
- 9.2. Endogenous vs. Exogenous Drivers of Spatial Ordering
- 9.3. Vicsek Model: Uniting Static and Dynamic Order
- 9.4. Collective Decision Making at the Flock Scale
- 9.5. Take-Home Messages
- 9.6. Homework Problems
- 9.7. Technical Appendix
- 10. Conflict and Cooperation Among Individuals and Populations
- 10.1. Games, Relatively Speaking
- 10.2. Payoffs: A Classic Approach
- 10.3. From Payoffs to Populations
- 10.4. Games that Real Organisms Play
- 10.5. Feedback Between Strategies and the Environment
- 10.6. Take-Home Messages
- 10.7. Homework problems
- 10.8. Technical Appendix
- 11. Eco-Evolutionary Dynamics
- 11.1. The Power of Exponentials
- 11.2. Canonical Models of Population Dynamics
- 11.3. Predator-Prey Dynamics
- 11.4. Toward Predator-Prey Dynamics with Rapid Evolution
- 11.5. Take-Home Messages
- 11.6. Homework Problems
- 11.7. Technical Appendix
- 12. Outbreak Dynamics: From Prediction to Control
- 12.1. Modeling in the Age of Pandemics
- 12.2. The Core Model of an Outbreak: The SIR Model
- 12.3. The Shape of an Outbreak
- 12.4. Principles of Control
- 12.5. EVD: A Case Study in Control Given Uncertainty
- 12.6. On the Ongoing Control of SARS-CoV-2
- 12.7. Take-Home Messages
- 12.8. Homework Problems
- 12.9. Technical Appendix
- IV. The Future of Ecosystems
- 13. Ecosystems: Chaos, Tipping Points, and Catastrophes
- 13.1. Ecosystems-the Integrated Frontier
- 13.2. Chaos in Communities
- 13.3. Condorcet and Catastrophes
- 13.4. Thresholds in Ecosystems and the Earth System
- 13.5. The Challenge Continues
- References
- Index
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