Chapter 1. Biological Thermodynamics: On Energy, Information and its Evil Twin, Entropy

1.1       Introduction

1.2       The Four Forces: Weak, Strong, Electromagnetic and Gravitational; An Emphasis on the Weak Force

1.3       Energy in Its Various Forms

1.4       Heat and Work

1.5       The Birth of Thermodynamics

1.6       Microscopic Origin of Entropy

1.7       The Rule of Law in Physics: Energy Conservation

1.8       The First and Second Laws of Thermodynamics

1.9       Energy Cannot Be Created but Can Be Transformed

1.10     Heat, Entropy and Energy Efficiency

1.11     Specific Heat

1.12     Thermodynamics of Mechanical Engines

1.13     The Carnot Engine

1.14     Enthalpy and Internal Energy – Compared and Contrasted

1.15     Gibbs Free Energy and the Chemical Potential

1.16     Thermodynamics of Biochemical Reactions

1.17     Information Energy

1.18     Thermodynamic Stability; Phase Transitions, Order Parameters and Susceptibility Functions

1.19     Expanded Concepts of Entropy and Information

1.20     How Information is Connected to Energy

1.21     Steady States and Homeostasis

1.22     Structures and Their Functions

1.23     Negative Entropy and Self-Organization

1.24     Biological Engines as Metaphors of the Carnot Engine

1.25     Metabolism: Life’s Necessity

1.26     How Metabolism is Linked to Aging

1.27     The Ultimate Source of Life’s Energy: Photosynthesis

1.28     The Difference Between Quantum and Classical Metabolism May Be the Difference Between Health and Disease

1.29     Thermodynamic Processes in Metabolism

1.30     Two Paths to Metabolic Energy Production

1.31     Inflammation, Pathogenesis and Obesity

1.32     Ecological Symbiosis of Plants and Animals

1.33     Metabolic Dysfunction and Disease States

1.34     Inflammation, Toxicity and Reactive Oxygen Species

1.35     What Can Einstein’s Theories of Relativity Tell Us About Aging?

1.36     Limitations of Scientific Reductionism and A Way Out

Chapter 3. From Quantum Biology to Quantum Medicine

3.1       On the Cusp of a Quantum Biology Revolution

3.2       A Historical Perspective on Physics

3.3       The Dawn of Quantum Biology

3.4       Decoherence

3.5       Quantum Weirdness and Biology

3.6       Can Objections to Quantum Biology Be Overcome?

3.7       The Appeal of Quantum Mechanisms to Biology

3.8       Biophotons: Light in Cells

3.9       Quantum Nature of Vision, Olfaction and Bird Navigation

3.10     Photosynthesis: Quantum Metabolism of Plants

3.11     Quantum Metabolism

3.12     Consequences of Quantum Metabolism

3.13     Synchronization of Cellular Activities

3.14     The Orchestra of Life: Biological Coherence

3.15     Biological Motors

3.16     Classical and Quantum Molecular Motors and the Laws of Thermodynamics

3.17     Energy and Information: A Marriage of Physics and Information Science in Biology

3.18     Classical and Quantum Information in Biology

3.19     Aging and Senescence

3.19.1  Machine Versus Biological Engine Analogy

3.19.2  Non-Redox Mediated Causes of Dysfunctional Oxidative Metabolism

3.19.3  Energy Transfer and Transformation of Information: Defense Against Biological Aging

3.20     Can Special Relativity Be of Relevance to Biology

3.21     Information and Nutrition

3.22     Chemical Potential of Physical Biological Systems

3.23     Is Consciousness A Quantum Phenomenon?

3.24     Brain’s Processing Power: How Many Flops and How Many Watts?

3.25     The Human Brain: its Structural Complexity and Amazing Efficiency

3.26     The Neuron: its Architecture and Central Role in the Brain’s Activities

3.27     The Special Role of Neuronal Microtubules and the Cytoskeleton

3.28     Where is Memory Stored in the Brain?

3.29     Are There Quantum Excitations in Microtubules?

3.30     Is Anesthesia a Quantum Process?

3.31     Relevance of Quantum Biology to Health and Disease

3.32     The Feasibility of Encoding the Totality of the Human Experience and the Information Field of the Brain

3.33     An Integrated Perspective of Energy and Information Flow in Health and Disease

Chapter 5. Introduction to The Roadmap of Future Medicine – The Physiological Fitness Landscape

5.1       Models Inspired by Physics Can Help with Understanding Biological Systems

5.1.1    A Free-Energy Landscape Model

5.1.2    Biological Motors as Mechanical Engines

5.1.3    Biological Thermodynamic Engines

5.1.4    Framing Energy by the Creation of Time and Life

5.2       The Bridge from Physics to Physiology and Medicine

5.2.1    Symmetry, Symmetry Breaking and Reductionism

5.2.2    Biological Mechanisms of Survival and Stress

5.2.3    Why Do We Need a New Medicine?

5.3       Creative Thinking, Information Transfer, and the Physiological Fitness Landscape

5.3.1    Physiological Fitness Landscape

5.3.2    Order Parameters, Control Parameters and Physiological Fitness Landscape for Disease State

5.3.3   An Example of Order and Control Parameters of Diabetes, The Classic Metabolic Disease

5.3.4    Physiological Fitness Landscape as a Guiding Concept in Medical Diagnosis

5.4       Physiological Fitness Landscape as an Organizing Principle for Understanding Health and Disease

5.4.1    Survival and Design Principles for Its Achievement

5.4.2    The Various Types of Stress and The Physiological Fitness Landscape

5.4.3    Main Features of the Physiological Fitness Landscape

5.4.4    Entropy Increase Along the Time Axis and Aging

5.4.5    Curing a Disease Is Not Reversed Aging

5.4.6    Summary

5.5       A Look at the Elements of the Metabolism Story

5.5.1    The Stress Response

5.5.2    Metabolism and the NHR Superfamily

5.5.3    The Biology of Time

5.5.4    Calorie Restriction, Intermittent Fasting, and Time-Restricted Feeding

5.5.5    The Microbiota

5.5.6    Insulin Resistance

5.5.7    Mitochondrial Function and Dysfunction and Insulin Resistance

5.5.8    Chronic Diseases of Aging as Metabolic Disorders

Chapter 2. Biological Engines and the Molecular Machinery of Life

2.1       Living Systems Viewed as Machines

2.2       Physical Forces in a Biological Context

2.3       Force and Energy Generation at the Organismic Level

2.4       Cell Energetics – The Cell as a Machine

2.5       Cell’s Tensional Integrity: Tensegrity

2.6       The Mechanics of Cell Motion: Cell Motility

2.7       Energy Production and Energy Transduction

2.8       Mitochondria

2.9       Chloroplasts

2.10     Osmotic Work

2.11     Energy and Material Transport In and Out of a Cell

2.11.1 Passive Transport

2.11.2 Active Transport

2.11.3 Ion Channels and Ion Pumps

2.12     The Cytoskeleton

2.13     Work During Cell Division: Chromosome Separation

2.14     Microtubules

2.15     Actin Filaments (Microfilaments)

2.16     Intermediate Filaments

2.17     The Quantum of Biological Energy: ATP

2.18     Molecular and Biological Machines: Motor Proteins

2.19     ATP Synthase

2.20     The Myosin Family of Motors

2.21     The Kinesin Family of Motors

2.22     Dynein

2.23     Energy Combustion Similarities Between Cells and Automobiles

2.24     Molecular Motors and the Laws of Thermodynamics

2.25     Analogy Between Mechanical and Biological Engines

2.26     Biological Thermodynamics

2.27     The Many Types of Biological Signals

2.28     Neuronal Signal Propagation

2.29     Electromagnetic Energy Across Scales of Biology

2.29.1  Bioenergetics: The Davydov Soliton

2.29.2 Biological Coherence: The Fröhlich Model

2.30     Electrodynamic Interactions in Biology

2.31     Charge Transport

2.32     Electric Field Effects Present in Cells and Acting on Cells

2.33     Ionic Current Flows Through Intra-Cellular Electrolytes

2.34     Proton Transport

2.35     Electron Conduction and Tunneling

2.36     Interactions of Biological Systems with Electromagnetic Radiation

2.37     Bioelectricity and Biomagnetism

2.38     Biological Engines and the Quantum Biological Processes Explaining Cognition

2.39     Connections Between Electricity, Magnetism and Energy Generation

2.40     Connections between Microtubules, Molecular Motors and Mitochondria; Toward a Molecular Explanation of Free Will

2.41     Collective Unconscious and Society

Chapter 4. From Systems Biology to Systems Medicine

4.1       Problem Solving – Reductionism versus Simplifying Complexity

4.2       Symmetries, Conservation Laws and Symmetry Breaking

4.3       Systems: Open and Closed, Simple and Complex

4.4       Stability, Biological Complexity, and Energy Flows

4.5       Implications for Clinical Practice

4.6       Framing Energy by the Creation of Time and Life, and by the Breaking of Symmetry

4.7       Steady States, Attractor States, Strange Attractors and Chaos

4.8       Nonlinear Interactions: Positive and Negative Feedback Loops

4.9       Why Life Exists: A Chaos Theory Perspective

4.10     A Pedestrian Overview of Systems Biology

4.11     Relevance of Chaos Theory to Human Biology

4.12     Self-Organization and Self-Regulation

4.13     Playing Simple Games with Profound Implications: Cellular Automata

4.14     Biological Networks

4.15     Simplifying Complexity

4.16     The Limitations in Molecular Biology and Reductionism in Explaining the Living World

4.17     Systems of Wholes and Parts

4.18     Complexity and Information

4.19     Nonlinearity, Bifurcations and Phase Transitions

4.20     A Biological Example: Metabolic Memory

4.21     Plus ça change, plus c’est la même chose

4.22     The Physics of Heat and the Biology of Inflammation: Are They Related?

4.23     Distinctions Between Homeostasis, Dynamic Equilibrium and Steady States

4.24     Classes of Systems: Biological and Man-Made

4.25     Application of Molecular Biology of Insulin Resistance and Type 2 Diabetes to Clinical Enigmas

4.26     Integrated Complexity of Systems Biology into an Optimally Functioning Whole

4.27     Systems Theory – A Perspective

4.28     Chaos Theory

4.29     Complicated Systems and Complex Systems

4.30     Bottom-up and Top-down Approaches

4.31     Algorithmic Medicine?

4.32     An Added Layer of Complexity: Gut Microbiome

4.33     Electronic Medical Records

4.34     An Anecdote Shared by Greg Shorr Regarding the Use of His Electronic Medical Record on the Native American Reservation

4.35     The Neuroendocrine and Immune System Hormonal Stress Responses: Adaptive Versus Pathologic and the Role of the Fitness Landscape Model

4.36     Concluding Remarks

4.37     An unsuspected trigger of mental status change

Chapter 6. Science Seen Through the Lessons of Life

6.1       A Bird’s Eye Overview of the Book’s Messages

6.2       Anecdotes and Their Morals

6.2.1    Anecdote 1: Football Teams

6.2.2    Anecdote 2: Synchronization in Music

6.2.3    Anecdote 3: The Power of Placebo

6.2.4    Anecdote 4: Human Interconnectedness

6.2.5    Anecdote 5: A 40-year old Professional Athlete 

6.3       The Essence of this Book’s Message

6.4       Understanding Biology and Medicine Through the Lens of Physics

6.5       Calming Words of Advice for the Patient

6.6       A Few Words About Free Will

6.7       On the Importance of Connections at All Levels

6.8       The Physiological Fitness Landscape and Politics

6.9       Striving for Balance Amongst Complexity

6.10     A New Perspective

6.11     The Bridge from Physiology to Spirituality