From the Atom to Living Systems : A Chemical and Philosophical Journey Into Modern and Contemporary Science

From the Atom to Living Systems represents an original historico-epistemological approach to follow the passage, in the microscopic analysis of reality, from the atomic to the molecular to the macromolecular levels and then to the threshold of life itself. Naturally, some parts of this journey have been developed in other works, some highly specialized and others of a more general nature. However, although this journey has often been traced in specialized scientific detail, the philosophical implications of the journey have not been discussed to any satisfactory degree. This scientific journey does have important philosophical consequences that constitute an integral part of this book, which is framed within the perspective of systems science and the so-called sciences of complexity, which are areas fundamental to 21st century science. In fact, the possibility of studying and understanding the material world through levels of complexity opens a great philosophical space that proposes to provide systemic and complex explanations, rather than reductive accounts that pretend to explain all phenomena through the interactions of elementary particles while considering all phenomena implicit and deterministic. The systemic and complex approach implies substituting unique bottom-up explanations, which move exclusively from the microscopically simple to the macroscopically complex, with a series of explanations that are horizontal within planes of complexity, vertically bottom up between various levels of complexity, vertically top-down, as well as circular in a manner that renders all levels of reality and the disciplines that study them as both autonomous and interconnected. Cover From the Atom to Living Systems Copyright Table of Contents Introduction: A Systemic Chemistry 1. Qualitative Atomism and Life within the 18th-​Century Atomistic Perspective Qualitative Corpuscularianism in the Renaissance and Early Modern Periods The Rejection of Hylomorphism and the Theory of Substantial Form Jan Baptista van Helmont and Qualitative Atomism The French Materialists and the Concept of Living Points 2. Early Modern Mechanistic Atomism and the Concept of Structure The Mechanistic Theory of Matter The Cartesian Mechanical Philosophy and the Denial of Substantial Form Pierre Gassendi and Mechanistic Atomism Robert Boyle and Form as Mechanistic Structure 3. Newton and the Newtonians Newton’s Relation to Cartesian Rationalism and Experimental Empiricism The Newtonian Reaction to Mechanistic Atomism The Leibnizian Programme and the Kantian Physical Monadology Boscovich’s Point Particles and the Unification of 18th-​Century Physics 4. Lavoisier and the Quantification of Chemistry The Concept of Element and the Fundamental Nature of Material Reality Lavoisier’s Empiricism and His Operational Concept of Element Lavoisier’s Quantification of Chemistry 5. Affinity, Compounds, and the Laws of Definite Proportions Geoffroy and Bergman on Affinity Berthollet’s Concepts of Chemical Compound and Variable Proportions Proust’s Classification of Substances and the Law of Definite Proportions 6. John Dalton and Chemical Atomism The Problem of Reconciling Elementarity with Atomicity The Weakness of Atomism for Experimental Science John Dalton Some Problems with Dalton’s Chemical Atomism 7. Valence, Chemical Bonds, and the Theory of Elements William Prout’s Hypothesis Regarding Atomic Weights Affinity, Valence, and Molecular Structure Mendeleev, the Periodic Table, and Theory of Elements 8. Organic Chemistry, Molecules, and the Implications for Atomism Background for the Molecular Structure Hypothesis Kekulé’s Concept of Transformation Formulae Atomic Bonding and Butlerov’s Structural Theory 9. The Relationship between Chemistry and Biology in the 19th Century Matter and the Processes of Living Beings Wöhler’s Artificial Synthesis of Urea The Dispute between Berthelot and Pasteur over Fermentation The Discovery of Buchner’s Cell-​Free Fermentation Energy/​Heat in Living and Physiological Chemistry Order/​Disorder and the Complexity of Living Beings: Finalism and the Evolution of Species in Darwin, Spencer, and Bergson 10. The Quantum Revolution Subatomic Particles and Atomic Structure The Concept of Atom in Quantum Mechanics Differences and Similarities between Classical and Quantum Atoms The Chemical Bond and the Molecule in Quantum Mechanics Characteristics of Contemporary Chemical Bonds 11. The Emergence of the Concept of Macromolecule The Protoplasmic Theory The Colloidal State Toward the Macromolecule In vitro and In vivo Protein Folding and Denaturation Philosophical Considerations on Protein Folding: System, Environment, and Self-​Organization Statistics and Self-​Organization Determination of Different Protein Structures Structure and Shape in Molecules and Macromolecules 12. From the Gene to Metagenomics: The Frontiers of Molecular Biology Mendel: An Innovator Rediscovered The Concept of the Gene The Materialization of the Gene: DNA The “Complexification” of DNA DNA as an Identity Factor of Living Species Epigenetics Metagenomics 13. Cellular Chemism The Cell: The Fundamental Unit of Living Beings The Internal State of the Cell The Cell’s Ability to Know and React to Its Environment A Code in the Cell and the Processes Connected to It Two Classes of Chemical Reactions in Cells Two Hypotheses of Enzyme Action The Energy Metabolism 14. What Is Life? The Chemical Perspective and Its Relation to Other Perspectives The Efficacy of the Chemical Approach to Life The Birth of Biosemiotics Open and Closed Systems Prigogine and the Thermodynamics of Nonequilibrium System-​Environment A Philosophical Consideration of What Is Life and Schrödinger’s Problem Conclusion Bibliography Index