Biology for engineers

Cover
Half Title
Title Page
Copyright Page
Dedication
Table of Contents
List of Examples
List of Tables
List of Boxes
Preface for First Edition
Preface for Second Edition
Acknowledgments for First Edition
Acknowledgments for Second Edition
Author
Section I: Introduction
	1: Introduction
		1.1 Introduction
		1.2 Science and Engineering
			1.2.1 Phylogeny
			1.2.2 Motivation
			1.2.3 Methods
			1.2.4 Synthesis
		1.3 Scientific Method
		1.4 Mathematical Modeling
			1.4.1 The Value of Models
			1.4.2 Types of Models
			1.4.3 Steps in the Modeling Process
			1.4.4 Models and Empirical Observations
		1.5 Biological Engineering
		1.6 Expectations for Biological Engineers
		1.7 About Predictions
		1.8 About This Book
		Questions
Section II: Principles from the Sciences
	2: Principles of Physics
		2.1 Effort and Flow Variables
			2.1.1 Resistance
			2.1.2 Capacity
			2.1.3 Inertia
			2.1.4 Efforts Required
		2.2 Balances
		2.3 States of Matter
			2.3.1 Gases
			2.3.2 Liquids
			2.3.3 Solids
			2.3.4 Gas Plasma
			2.3.5 Phase Changes
		2.4 Equivalence of Work and Energy
			2.4.1 Work
			2.4.2 Energy
			2.4.3 Efficiency
		2.5 Free Energy
			2.5.1 Internal Energy
			2.5.2 Enthalpy
			2.5.3 Entropy
			2.5.4 Gibbs Free Energy
		2.6 Disorder and Entropy
		2.7 Heat Transfer
		2.8 Movement of Materials
			2.8.1 Convection and Diffusion
			2.8.2 Osmosis
		2.9 Fluid Mechanics
			2.9.1 Viscosity
			2.9.2 Fluid Movement
			2.9.3 Fluid Energy
			2.9.4 Circulatory System
			2.9.5 Static Pressure
		2.10 Solid Mechanics
			2.10.1 Inertia
			2.10.2 Acceleration
			2.10.3 Reaction Forces
			2.10.4 Stress
		2.11 Electricity
			2.11.1 Electrostatics
			2.11.2 Electrical Current
			2.11.3 Electrical Power
		2.12 Temperature Effects
		Questions
	3: Principles of Chemistry
		3.1 Periodic Nature of Elements
		3.2 Chemical Bonding
			3.2.1 Ionic Bonds
			3.2.2 Covalent Bonds
			3.2.3 Electronegativity
			3.2.4 Water as a Polar Molecule
			3.2.5 Hydrogen Bonds
			3.2.6 van der Waals Forces
		3.3 Chemical Equilibrium
		3.4 Acids and Bases
			3.4.1 Strong and Weak Acids and Bases
			3.4.2 Salts
			3.4.3 pH
		3.5 Reaction Rates
			3.5.1 Collision Theory
			3.5.2 Intermediate Reactions
			3.5.3 First-Order Reactions
			3.5.4 Enzyme–Substrate Reactions
		3.6 Carbon Chemistry
			3.6.1 Many Possible Configurations
			3.6.2 Functional Groups
			3.6.3 Amino Acids
			3.6.4 Macromolecule Types
			3.6.5 Polymers
			3.6.6 Melting and Boiling Points
			3.6.7 Organic Reactions
		3.7 Physical Chemistry in Water
			3.7.1 Solutions
			3.7.2 Gels
			3.7.3 Suspensions
			3.7.4 Isoelectric Point
		3.8 Protein Folding
		3.9 Shape Effects and Enzymes
		3.10 Energy-Rich Compounds
		3.11 Temperature and Pressure Effects
		3.12 Free Energy
		Questions
	4: Principles of Mathematics and Engineering Sciences
		4.1 Equality
		4.2 Randomness and Probability
			4.2.1 Probability Distributions
			4.2.2 Self-Similar Data
			4.2.3 Pseudorandom Data
			4.2.4 Statistics
		4.3 Calculus
			4.3.1 Derivatives and Differential Equations
			4.3.2 First-Order Equations
			4.3.3 Exponential Responses
			4.3.4 Second-Order Equations
			4.3.5 Periodicity
			4.3.6 Nonlinear and Nonconstant Equations
			4.3.7 Integration
		4.4 Control Systems
			4.4.1 Sensors
			4.4.2 Actuators
			4.4.3 Communications
			4.4.4 Closed-Loop Feedback Systems
			4.4.5 Open-Loop Systems
			4.4.6 Closed-Loop Feedforward Systems
			4.4.7 Adaptive Control Systems
			4.4.8 Fuzzy Control Systems
		4.5 Optimization
		4.6 Information
		4.7 Analog and Digital Signal Processing
		Questions
	5: Principles of Biology
		5.1 Form and Function
		5.2 Modularity and Incremental Change
		5.3 Genetic Basis
			5.3.1 DNA as the Blueprint
			5.3.2 RNA as the Fabricator
			5.3.3 Gene Types
			5.3.4 Genetic Expression
			5.3.5 Epigenetics
			5.3.6 RNA Interference
			5.3.7 Antisense Molecules and Omics
			5.3.8 Genetic Variation
			5.3.9 Replication
			5.3.10 Mutations
			5.3.11 RNA Correcting DNA
			5.3.12 Mitochondrial and Chloroplast DNA
			5.3.13 Plasmid DNA
		5.4 Competition and Selection
		5.5 Biological Hierarchies
			5.5.1 The Cell
			5.5.2 What Is Life?
			5.5.3 Synthetic Biology
			5.5.4 Ecology on Micro- and Macroscales
			5.5.5 Food Pyramid
		5.6 Is Biology Complex or Simple?
		Questions
Section III: Responses of Living Systems
	6: Biological Responses in Context
		6.1 Biological Units Need Water
			6.1.1 Water Has Unique Properties
			6.1.2 Water Surrounding Biological Units
			6.1.3 Water Balance
			6.1.4 Biological Units Barriers to Water Movement
		6.2 Biological Units Need the Right Amount of Oxygen
			6.2.1 Anaerobes and Facultative Anaerobes
			6.2.2 Oxidative Metabolism
			6.2.3 Oxygen Delivery
			6.2.4 Too Much Oxygen
		6.3 Biological Units Need Food and Nutrients
			6.3.1 Essential Elements
			6.3.2 Food and Nutrients for Energy and Essential Biochemicals
			6.3.3 Microbes Assist Digestion
			6.3.4 Synthetic Growth Media
		6.4 Biological Units Become Ill in the Presence of Wastes
		6.5 Biological Units Need Heat Sources and Sinks
			6.5.1 Heat Sources
			6.5.2 Removing Excess Heat
			6.5.3 Moving to a Better Neighborhood
			6.5.4 The Best Thermal Conditions
			6.5.5 Too Hot
			6.5.6 Too Cold
		6.6 Biological Units Adapt to Their Environments
			6.6.1 Cells and Microbes
			6.6.2 Hypertension
			6.6.3 Color Changes
			6.6.4 Adaptations to Light
			6.6.5 Other Adaptations
		6.7 Biological Units Modify Their Environments
		6.8 Adaptations Require Extra Energy and Resources
		6.9 Biological Units, If Possible, Move to Friendlier Environments
		6.10 Biological Units Evolve under Environmental Pressures
		6.11 Crowding of Biological Units Produces Stress
			6.11.1 Antisocial Behavior
			6.11.2 Crowding in Humans
			6.11.3 Personal Space
			6.11.4 Sensory Overload
			6.11.5 Animal Spaces and Animal Welfare
			6.11.6 Crowding and Disease
			6.11.7 Densities in the Wild
		6.12 Biological Units Are Affected by Chemical Stresses
			6.12.1 Toxicity
			6.12.2 Dose–Response
			6.12.3 High Doses
			6.12.4 Metabolic Wastes
			6.12.5 Nanoparticles
			6.12.6 Toxins Used as Defenses
			6.12.7 Toxin Tolerances
			6.12.8 Toxin Concentration
			6.12.9 Endocrine Disruption
		6.13 Biological Units Respond to Mechanical Stresses
			6.13.1 Sedimentation and Clotting
			6.13.2 Strengthening and Stiffening
			6.13.3 Critical Shear Stress
			6.13.4 Stem Cell Substrates
			6.13.5 Whole Plant Responses
			6.13.6 Bodies in Motion
		6.14 Optimization Is Used to Save Energy and Nutrient Resources
			6.14.1 Reproductive Advantage
			6.14.2 Locomotion
			6.14.3 Breathing and Heart Rate
			6.14.4 Genetic Variability
			6.14.5 Ecological Optimization
			6.14.6 Mode of Action
		6.15 Biological Units Alter Themselves to Protect against Harsh Environments
			6.15.1 Torpor, Hibernation, and Estivation
			6.15.2 Endospores
			6.15.3 Seeds and Spores
			6.15.4 Plant Responses
			6.15.5 Response to Hemorrhage
			6.15.6 Psychological Trauma
		6.16 Biological Units Cooperate with Other Biological Units
			6.16.1 Symbiosis
			6.16.2 Coevolution
			6.16.3 Plant Reproduction
			6.16.4 Communal Benefit
			6.16.5 Inadvertent Benefit
		6.17 Biological Units Compete with Other Biological Units
			6.17.1 Plants and Herbivores
			6.17.2 Predators
			6.17.3 Parasites
			6.17.4 Pathogens
		6.18 Biological Units Reproduce
			6.18.1 Asexual Reproduction
			6.18.2 Exchange of Bacterial Genes
			6.18.3 Somatic Cell Reproduction
			6.18.4 Telomeres
			6.18.5 Sexual Reproduction
			6.18.6 Courtship
			6.18.7 External or Internal Fertilization
			6.18.8 Hermaphrodites
			6.18.9 Plant Reproduction
		6.19 Biological Units Coordinate Activities through Communication
			6.19.1 Acoustic Stimuli
			6.19.2 Chemical Stimuli
			6.19.3 Touch Stimuli
			6.19.4 Visual Stimuli
			6.19.5 Others
			6.19.6 Just Noticeable Difference
		6.20 Biological Units Maintain Stability with Exquisite Control
			6.20.1 The Senses
			6.20.2 Controllers
			6.20.3 Redundancy
			6.20.4 Antagonistic Action
			6.20.5 Dead Zone
			6.20.6 Time Delays
			6.20.7 Working with Biological Control
		6.21 Biological Units Go Through Natural Cycles
			6.21.1 Regeneration
			6.21.2 Maturation
			6.21.3 Senescence
			6.21.4 Death
			6.21.5 Annual Cycles
			6.21.6 Monthly Cycles
			6.21.7 Diurnal Cycles
			6.21.8 Cycles Shorter than a Day
			6.21.9 Asynchronous Nutrient Cycles
		6.22 Biological Units Need Emotional Satisfaction and Intellectual Stimulation
			6.22.1 The Nature of Emotions
			6.22.2 Personality
			6.22.3 Neurotransmitters
			6.22.4 Interpersonal Interactions
			6.22.5 Brain Development and Learning
			6.22.6 Psychological Hierarchy
			6.22.7 Social Infrastructure
			6.22.8 Mind–Body Interactions
		6.23 Biological Units Die
			6.23.1 What Does “Dead” Mean?
			6.23.2 Reliability Theory and Death Rates
			6.23.3 Is There a Natural Limit to Life Span?
		Questions
Section IV: Scaling Factors
	7: Allometric Relationships
		7.1 Allometric Relationships from Evolutionary Pressure
		7.2 Dimensional Analysis
		7.3 Golden Ratio
		7.4 Fractal Scaling within an Organism
			7.4.1 Body Mass
			7.4.2 Body Surface Area
			7.4.3 Body Dimensions
			7.4.4 Metabolic Rate and Related Temperatures
			7.4.5 Oxygen Consumption
			7.4.6 Heat Loss
			7.4.7 Cardiovascular Factors
			7.4.8 Respiration
			7.4.9 Walking and Running
			7.4.10 Relations Involving Time
			7.4.11 Food and Waste
			7.4.12 Bird Songs
			7.4.13 Plant Growth
		7.5 Self-Similarity for Tissues and Organs
			7.5.1 Organs
			7.5.2 Tissues
		7.6 Self-Similarity in Populations
			7.6.1 Number of Species
			7.6.2 Species Range
			7.6.3 Population Densities
			7.6.4 Population Doubling Time
		Questions
Section V: Utilizing Living Systems
	8: Biological Engineering Solutions
		8.1 Systems Approach
		8.2 Relationships between Engineering and Biology
			8.2.1 Living Things as the Solution (Bionics, or Hybrid Systems)
			8.2.2 Living Things as Models (Biomimetics)
			8.2.3 Biological Solutions to Biological Problems (Biotechnology)
			8.2.4 Living Things as Recipients (Biomedical Engineering)
			8.2.5 Living Things Inadvertently Affected
		8.3 The Completed Design
		8.4 Dénouement
		Questions
Appendix
References
Index