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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 communitiesStand-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 derivationsSuitable 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
Preface
Quantitative Biosciences at All Scales of Life
The Goal
The Structure of this Book
You Can Do It
Acknowledgments
Molecular and Cellular Biosciences
Fluctuations and the Nature of Mutations
Chance Favors the Independent Mutation
Cellular Phenotypes
Mutations that Depend on Selection
Independent Mutations: A Continuous Model
Modeling the Growth of (Discrete) Mutants
Variance of Mutants When Mutations are Independent of Selection
On (In)Direct Inference
Take-Home Messages
Homework Problems
Technical Appendix
Bistability of Genetic Circuits
More is Different
Molecular Cast and Scene
The First Ingredient: Regulation of a Target Gene
Feedback and Bistability—Autoregulation
The Dynamics of a Genetic Toggle Switch
Take-Home Messages
Homework Problems
Technical Appendix
Stochastic Gene Expression and Cellular Variability
Living with Randomness
Stochasticity in Gene Regulation
Characterizing Dynamics of Individual Cells, Given Stochastic Gene Expression
Is Gene Expression Bursty?
The Geometry of Bursts
Take-Home Messages
Homework Problems
Technical Appendix
Evolutionary Dynamics: Mutations, Selection, and Diversity
Evolution in Action
Selection and the Disappearance of Diversity
Mechanisms that Restore Diversity
Stochasticity in the Evolution of Populations—Baseline Expectations
Evolutionary Dynamics with Stochasticity and Selection
Sweeps or Hitchhiking or Both?
Take-Home Messages
Homework Problems
Technical Appendix
Organismal Behavior and Physiology
Robust Sensing and Chemotaxis
On Taxis
Why Swim?
The Behavior of Swimming E coli
Chemotaxis Machinery
Signaling Cascades
Fine-Tuned Adaptation
Buffering and Robust Cellular Adaptation
Take-Home Messages
Homework Problems
Technical Appendix
Nonlinear Dynamics and Signal Processing in Neurons
Walking in the Path of Hodgkin and Huxley
The Brain: Memory, Learning, and Behavior
Of Ions and Neurons
Dynamical Properties of Excitable Neuronal Systems
From Neurons to Neural Networks and Information Processing
Take-Home Messages
Homework Problems
Technical Appendix
Color Plates
Excitations and Signaling from Cells to Tissue
From Excitable Cells to Excitable Systems
Principles of Oscillatory Dynamics
Relaxation Oscillations—a Generalized View
Principles of Excitability: From Cardiac Cells to Tissue
Take-Home Messages
Homework Problems
Technical Appendix
Organismal Locomotion through Water, Air, and Earth
Movement from Within
Movement with Brief Moments in Air
Principles of Slow Swimming
Terrestrial Locomotion
Take-Home Messages
Homework Problems
Technical Appendix
Populations and Ecological Communities
Flocking and Collective Behavior: When Many Become One
Life is with Other Organisms
Endogenous vs Exogenous Drivers of Spatial Ordering
Vicsek Model: Uniting Static and Dynamic Order
Collective Decision Making at the Flock Scale
Take-Home Messages
Homework Problems
Technical Appendix
Conflict and Cooperation Among Individuals and Populations
Games, Relatively Speaking
Payoffs: A Classic Approach
From Payoffs to Populations
Games that Real Organisms Play
Feedback Between Strategies and the Environment
Take-Home Messages
Homework problems
Technical Appendix
Eco-Evolutionary Dynamics
The Power of Exponentials
Canonical Models of Population Dynamics
Predator-Prey Dynamics
Toward Predator-Prey Dynamics with Rapid Evolution
Take-Home Messages
Homework Problems
Technical Appendix
Outbreak Dynamics: From Prediction to Control
Modeling in the Age of Pandemics
The Core Model of an Outbreak: The SIR Model
The Shape of an Outbreak
Principles of Control
EVD: A Case Study in Control Given Uncertainty
On the Ongoing Control of SARS-CoV-
Take-Home Messages
Homework Problems
Technical Appendix
The Future of Ecosystems
Ecosystems: Chaos, Tipping Points, and Catastrophes
Ecosystems—the Integrated Frontier
Chaos in Communities
Condorcet and Catastrophes
Thresholds in Ecosystems and the Earth System
The Challenge Continues
References
Index