Chemistry inherits its subject matter from physics. The atoms whose combinations chemistry investigates are the atoms whose internal structure physics describes, and the forces that hold molecules together are electromagnetic forces whose character quantum mechanics specifies. The inheritance is acknowledged within chemistry and treated as unproblematic. Chemistry also takes the existence of atoms with particular properties as its starting point and proceeds to investigate what those atoms do when they encounter one another under varying conditions of temperature, pressure, and concentration. The investigation has produced a comprehensive body of knowledge. The substances that compose the physical world, from water to hemoglobin to the silicate minerals of the earth's crust, have been characterized with a precision that permits their synthesis, manipulation, and transformation according to plan. The discipline's practical success is visible in pharmaceuticals, materials, agriculture, and every domain where the behavior of matter at the molecular level determines outcomes. The starting point of the discipline, however, is a collection of givens. The atoms are there. They have certain properties. Chemistry begins after these facts are established and investigates what follows from them. Why are there atoms with these properties? The question falls to physics, which does not answer it. The concept of the chemical element emerged slowly from centuries of investigation into what matter is made of. Lavoisier's work in the late eighteenth century established the principle that matter is conserved in chemical reactions and identified a set of substances that could not be decomposed into simpler components by any known chemical means. [Lavoisier, Traité Élémentaire de Chimie, 1789] These substances he called elements, and his list, though imperfect by modern standards, established the framework within which chemistry would operate. An element was defined by what it resisted. If a substance could not be broken down further through chemical processes, it was elementary. The definition was operational. It described a limit of method, the point where chemical decomposition stopped, and the stopping point was taken to indicate something fundamental about the substance itself. Dalton formalized the relationship between elements and atoms in the early nineteenth century, proposing that each element consisted of identical atoms of a characteristic weight and that chemical compounds were formed by the combination of atoms in fixed ratios. [Dalton, A New System of Chemical Philosophy, 1808] The proposal unified a large body of chemical observation and gave chemistry a theoretical basis in discrete, countable entities. The atoms were the primitives of the theory. They could be counted, weighed indirectly through their combining ratios, and classified by their properties. Their existence was assumed. Dalton did not explain why atoms existed or why they had the specific weights and combining properties they displayed. The theory explained the regularities of chemical combination by positing entities whose own existence was taken as given. Mendeleev's periodic table, published in 1869, organized the known elements according to their atomic weights and demonstrated that their chemical properties recurred at regular intervals. [Mendeleev, "On the Relationship of the Properties of the Elements to their Atomic Weights," Zeitschrift für Chemie, 1869] The table organized existing knowledge into a coherent structure and revealed relationships among elements that had previously appeared unrelated. It also generated predictions about elements not yet discovered. Mendeleev left gaps in his table where the pattern demanded elements that no one had yet identified, and he specified the properties those elements would have. The subsequent discovery of gallium, scandium, and germanium, with properties matching Mendeleev's predictions closely, confirmed the table's power and established it as chemistry's central organizing framework. The table has since been refined through the understanding of atomic number, the quantity of protons in the nucleus, which replaced atomic weight as the organizing principle after Moseley's X-ray experiments in 1913. [Moseley, "The High Frequency Spectra of the Elements," Philosophical Magazine, 1913] The modern periodic table arranges 118 confirmed elements by atomic number, and the arrangement reveals the electronic structure that determines chemical behavior. Elements in the same column share similar outer electron configurations and therefore similar chemical properties. The table's predictive success has been confirmed across more than a century and a half of experimental work. Yet the table organizes what already exists. It describes regularities in the properties of atoms whose proton counts and electron configurations follow from quantum mechanical principles already in operation.
The periodic table organizes chemical reality. The reality it organizes is given, however. Why are there elements at all, and why do they have the properties the table so elegantly organizes? The table cannot address these questions because the table begins where those questions end. The understanding of why elements have the properties they do advanced decisively with quantum mechanics. The electronic structure of atoms, which determines their chemical behavior, follows from the solutions to the Schrödinger equation for electrons in the electrostatic field of the nucleus. The solutions yield orbitals, regions of probability where electrons are likely to be found, and the shapes and energies of these orbitals determine how atoms bond. The Aufbau principle, which describes how electrons fill orbitals in order of increasing energy, together with the Pauli exclusion principle, which prevents two electrons from occupying the same quantum state, generates the structure of the periodic table from quantum mechanical first principles. The electron configurations that Mendeleev's table organized empirically can be derived from the physics of quantum systems, though the derivation requires approximations for all but the simplest atoms. This derivation represents a major unification in natural science. Chemistry's regularities follow from physics. Physics provides the deeper account. The atoms whose properties the periodic table organizes behave as they do because of quantum mechanical laws operating on charged particles. The explanation traces chemical behavior to physical principles, and the tracing is legitimate and informative. The physical principles themselves remain unexplained within physics, from the specific form of the Schrödinger equation and the values of its constants to the existence of charged particles obeying these equations.
Chemical bonding demonstrates this dependence in detail. The covalent bond, in which atoms share electrons, was first described in quantum mechanical terms by Heitler and London in their treatment of the hydrogen molecule in 1927. [Heitler and London, "Interaction of Neutral Atoms and Homopolar Binding," Zeitschrift für Physik, 1927] Their calculation showed that two hydrogen atoms at a certain distance apart have lower energy when their electron wave-functions overlap constructively than when the atoms are separated, and that this energy difference constitutes the bond. Pauling extended this work into a comprehensive theory of chemical bonding, developing the concepts of hybridization, resonance, and electronegativity that remain central to how chemists understand molecular structure. [Pauling, The Nature of the Chemical Bond, Cornell University Press, 1939] Pauling's electronegativity scale, which quantifies the tendency of atoms to attract electrons in a bond, enabled predictions about the character of bonds between different elements and provided a framework for understanding the geometry of molecules. The ionic bond, in which electrons are transferred from one atom to another, and the metallic bond, in which electrons are delocalized across a lattice of atoms, received similar quantum mechanical treatment. In each case, the bond is understood as a consequence of the electromagnetic interaction between charged particles governed by quantum mechanics. The understanding is powerful and has enabled chemists to design new molecules, predict reaction products, and develop materials with specified properties. The understanding also has a specific character. It explains how bonds form given that atoms exist with the quantum mechanical properties they possess. The existence of those atoms, together with the specific charges, masses, and electromagnetic interactions involved, enters the explanation as unexplained input. Chemistry explains what atoms do with each other. Why atoms exist to do anything at all lies beyond the reach of the explanation. Carbon occupies a singular position within chemistry, and the position clarifies the discipline's relationship to the existential question. Carbon forms four covalent bonds and can bond with itself to produce chains and rings of immense variety. The number of known carbon compounds exceeds the number of compounds formed by all other elements combined. Organic chemistry, the study of carbon compounds, constitutes the largest subdivision of chemistry and provides the molecular basis for biology. The versatility of carbon follows from its electronic structure. With four valence electrons and an electronegativity that permits bonding with elements across a wide range of the periodic table, carbon can form single, double, and triple bonds, and the tetrahedral geometry of its single bonds allows for three-dimensional molecular structures of essentially unlimited complexity. Friedrich Wöhler's synthesis of urea from inorganic precursors in 1828 demonstrated that organic compounds did not require a vital force for their production, collapsing the distinction between organic and inorganic chemistry that had previously been assumed fundamental. [Wöhler, "On the Artificial Production of Urea," Annalen der Physik und Chemie, 1828] The synthesis opened a domain of investigation that has grown continuously since. The molecular diversity that carbon chemistry produces underlies the biochemistry of every known living organism. The diversity follows from the properties of carbon, and those properties follow from quantum mechanics. Why does the universe contain an element with precisely these bonding characteristics? Physics answers the question partially. The answer traces carbon's properties to the physics of the strong nuclear force, which permits the formation of carbon-12 nuclei, and to quantum mechanics, which determines the electron configuration that makes carbon so versatile in bonding. The derivation is legitimate and precise. It terminates at the laws of physics and the constants that govern nuclear and electromagnetic interactions, and those laws and constants are where the explanation stops without explaining itself. The properties of molecular substances often differ dramatically from the properties of their constituent elements. Water provides the most familiar example. Hydrogen is a flammable gas and oxygen supports combustion, yet water extinguishes fire. The properties of the compound bear little resemblance to the properties of the elements, and the emergence of novel properties through combination is characteristic of chemistry at every level. The phenomenon is sometimes discussed under the heading of emergence, a term that carries philosophical weight beyond its chemical usage. Within chemistry, the emergence of molecular properties from atomic constituents is well understood in principle. The properties of water, from its liquid state at room temperature and high specific heat capacity to its effectiveness as a solvent for ionic compounds, follow from the geometry of the water molecule and the polarity of the O-H bonds, which in turn produce hydrogen bonding between molecules. The hydrogen bonds are weaker than covalent bonds but strong enough to impose structure on liquid water and to account for many of its anomalous properties, including the fact that ice is less dense than liquid water, an anomaly with profound consequences for the habitability of the earth. The explanation traces macroscopic properties through molecular geometry to quantum mechanical principles. The explanation succeeds on its own terms. At no point in the tracing does the question of why molecules have these properties, or why quantum mechanics and its constants take the specific form that produces hydrogen bonding with these particular characteristics, receive treatment. The emergence of water's properties from its molecular structure is explained. The existence of a world in which molecular structure produces properties at all is assumed throughout. Thermodynamics provides chemistry with its framework for understanding why reactions occur and in what direction they proceed. The laws of thermodynamics, formulated in the nineteenth century by Clausius, Kelvin, Boltzmann, and Gibbs among others, describe the relationships between energy, entropy, and temperature that govern all physical and chemical processes. The first law establishes the conservation of energy. The second law establishes that entropy in an isolated system tends to increase, providing the directionality that distinguishes processes that occur spontaneously from those that do not. Gibbs synthesized these principles into the concept of free energy, a quantity that combines the energetic and entropic contributions to determine whether a chemical reaction will proceed under given conditions. [Gibbs, "On the Equilibrium of Heterogeneous Substances," Transactions of the Connecticut Academy, 1878] A reaction proceeds spontaneously when it decreases the Gibbs free energy of the system, and equilibrium is reached when free energy is minimized. The framework has broad explanatory reach. It applies to every chemical reaction, from the combustion of fuels to the folding of proteins, and it enables prediction of equilibrium compositions, phase transitions, and the feasibility of industrial processes. The framework also rests on laws whose status deserves attention. The laws of thermodynamics describe regularities that hold throughout the physical world. Their universality has been confirmed across every domain where they have been tested. The universality itself, however, is a fact about the world that thermodynamics describes and does not explain. Why does energy conserve? Why does entropy tend to increase? Statistical mechanics, developed by Boltzmann and refined by Gibbs and others, derives the second law from the behavior of large numbers of particles, showing that the increase of entropy is overwhelmingly probable given the statistical properties of many-particle systems. [Boltzmann, Lectures on Gas Theory, Cambridge University Press, 1896] The derivation is substantial, as it reduces a macroscopic law to the statistical behavior of microscopic constituents. The microscopic constituents are particles whose existence and properties are given. The laws of probability that govern their collective behavior are also given. The derivation explains thermodynamic regularity by appealing to particles and statistics, and the particles and statistics are themselves unexplained starting points. Chemical kinetics, the study of reaction rates, illustrates a further dimension of chemistry's explanatory structure. The Arrhenius equation, developed in the late nineteenth century, describes how reaction rates depend on temperature through an activation energy that reactants must overcome for the reaction to proceed. [Arrhenius, "On the Reaction Velocity of the Inversion of Cane Sugar by Acids," Zeitschrift für Physikalische Chemie, 1889] Transition state theory, developed by Eyring and by Evans and Polanyi in the 1930s, provided a quantum mechanical account of the activated complex through which reactants pass on their way to products. [Eyring, "The Activated Complex in Chemical Reactions," Journal of Chemical Physics, 1935] The theory connects the macroscopic observable of reaction rate to the microscopic physics of molecular encounters, and the connection has proven robust across an enormous range of chemical systems. The theory explains why some reactions are fast and others slow, why catalysts work, and how temperature affects the transformation of matter. Every element of the theory presupposes molecules with specific properties, governed by physical laws that determine how those molecules interact across varying energy configurations. The theory explains the dynamics of transformation within existence. Transformation presupposes things that transform, and the existence of those things is where the theory begins.
The natural sciences that study the earth and its systems inherit these assumptions in another instance. Geology investigates the composition, structure, and history of the earth through methods that assume the existence of matter with the properties chemistry describes. Hutton, writing in the late eighteenth century, established the principle of uniformitarianism, the idea that the processes observable in the present, erosion, sedimentation, volcanic activity, are the same processes that shaped the earth in the past. [Hutton, Theory of the Earth, 1795] Lyell developed this principle into a comprehensive framework for interpreting the geological record, demonstrating that rock stratification, fossil distribution, and the configuration of the earth's surface could be understood through processes operating over vast stretches of time. [Lyell, Principles of Geology, John Murray, 1830] The framework transformed the understanding of the earth's history and established geology as a historical science capable of reconstructing events millions and billions of years in the past. The reconstruction depends at every point on the assumption that matter existed throughout those vast periods with the properties it currently displays. Minerals form through chemical processes. Rocks are classified by their mineral composition and the conditions under which they formed. The rock cycle, tracing the transformation of igneous rock to sedimentary rock to metamorphic rock and back, describes a continuous process of transformation that has operated throughout the earth's history. The entire description presupposes atoms that combine into minerals and then into rocks, all governed by physical laws determining the temperatures and pressures under which transformations occur. Geology explains the history of the planet. The existence of an Earth with a history, composed of matter that obeys particular physical and chemical laws, is the starting condition of the explanation. Plate tectonics, the unifying theory of modern geology, describes the movement of the earth's lithospheric plates and provides a framework for understanding earthquakes, volcanism, mountain building, and the configuration of continents. [Wegener, The Origin of Continents and Oceans, 1915; Hess, "History of Ocean Basins," Petrologic Studies, 1962] The theory was confirmed through multiple lines of evidence including paleomagnetic data, the distribution of earthquakes and volcanoes along plate boundaries, and the patterns of seafloor spreading documented by Vine and Matthews. [Vine and Matthews, "Magnetic Anomalies over Oceanic Ridges," Nature, 1963] The explanatory power of plate tectonics extends across geology. It connects phenomena that appear unrelated, from continental fit and fossil distribution to the location of mineral deposits, into a single coherent account of the earth's dynamic surface. The account operates entirely within the assumption that the earth exists as a physical body composed of matter with known properties, heated by radioactive decay in its interior, and subject to the laws of physics that govern convection and material deformation. Each element of the explanation presupposes things, properties, and laws already in place. The explanation succeeds within that framework. The framework itself is given. Geochemistry traces the distribution of elements through the earth's systems, from the primordial nucleosynthesis in stellar interiors that produced the heavy elements, through the accretion of the solar system from the solar nebula, to the ongoing cycling of elements through the earth's crust, mantle, oceans, and atmosphere. Victor Goldschmidt's classification of elements by their geochemical behavior, distinguishing lithophile, siderophile, chalcophile, and atmophile elements based on their affinity for silicate, metal, sulfide, or gaseous phases, provided a framework for understanding why certain elements concentrate in certain geological environments. [Goldschmidt, Geochemistry, Oxford University Press, 1954] The framework connects the chemistry of the elements to the large-scale structure of the planet. Iron sinks to the core because of its density and its siderophile character. Silicon and aluminum concentrate in the crust because of their lithophile behavior. The distribution follows from the chemical and physical properties of the elements under the conditions that prevailed during the earth's formation and differentiation.
The explanation is satisfying within its domain. It traces the present distribution of elements to the processes that distributed them, and the processes to the properties of matter under known physical conditions. Every step of the explanation presupposes elements with properties, a planet forming from a nebula that already contained those elements, and physical laws governing the entire process. Geochemistry explains how the earth came to have its present chemical composition. The existence of elements with specific properties, a nebula from which to form, and laws governing the process remains given throughout.
Atmospheric science and oceanography extend the pattern into the earth's fluid envelopes. The atmosphere is a mixture of gases whose composition, circulation, and chemistry determine weather, climate, and the conditions for life. The Navier-Stokes equations describing fluid dynamics, radiative transfer theory, and the thermodynamics of phase changes all derive from the physical and chemical properties of matter. Climate science, which integrates atmospheric, oceanic, cryospheric, and terrestrial processes into models of the earth system, represents one of the most ambitious applications of the natural sciences. The models are complex, incorporating feedbacks among components that operate on different timescales, and they have demonstrated skill in reproducing observed climate variations and in projecting future changes under different scenarios. [Manabe and Wetherald, "Thermal Equilibrium of the Atmosphere with a Given Distribution of Relative Humidity," Journal of the Atmospheric Sciences, 1967] The sophistication of the models reflects that of the science that produces them. It operates throughout on the assumption that an atmosphere of particular composition exists on a physical planet in a gravitationally governed solar system, and that the gases composing it interact with radiation and with each other according to known physical laws. The models describe how the Earth's climate system works. Why there is a planet with a climate system and atmosphere, falls outside the scope of the inquiry. The pattern extends through every natural science. Mineralogy classifies minerals by their crystal structure and chemical composition, investigating how atoms arrange themselves into the regular lattices that produce the physical properties of hardness, cleavage, luster, and optical behavior. The classification assumes atoms that form such lattices. Soil science addresses a different scale, studying the complex mixtures of minerals, organic matter, water, and air that support terrestrial ecosystems, and presupposing the minerals that weather, the organisms that decompose, and the water that transports dissolved substances. Hydrology traces the distribution and movement of water through the Earth system, from precipitation through surface flow and groundwater to eventual evaporation and atmospheric recycling. Its subject matter requires water with particular physical and chemical properties, terrain through which water flows, and an energy source driving evaporation. Each discipline takes the existence of its subject matter as given and investigates how that subject matter behaves. The assumptions differ in each case. The dependence runs from hydrology's reliance on water and terrain, through soil science's starting point in minerals and organisms, back to mineralogy's primitives of atoms and bonding. The entire sequence traces back through chemistry to physics, and physics does not explain why there is anything for any of these disciplines to study. Chemistry's relationship to physics deserves particular attention because it illustrates how the deferral of the existential question operates across disciplinary boundaries. When chemistry encounters its own limits, when the question of why atoms have the properties they do presses beyond what chemical methods can address, the discipline defers to physics. The deferral is legitimate and productive. Physics does provide deeper accounts of atomic structure, bonding, and the forces that govern molecular behavior. The accounts trace chemical phenomena to quantum mechanical principles with considerable explanatory success. The deferral pattern is natural and epistemically sound within the structure of scientific explanation. Each discipline explains phenomena within its scope and defers deeper questions to more fundamental disciplines. The pattern becomes significant at the point where the sequence of deferrals terminates. Chemistry defers to physics. Physics, in its most fundamental formulations, arrives at primitives, quantum fields, fundamental constants, laws of nature, that it can describe with exacting precision and cannot explain. The sequence of legitimate deferrals, each productive within its domain, ends at a discipline that acknowledges its own primitives as unexplained. The question of existence passes through chemistry to physics and receives no answer there. Peter Atkins, in his widely used physical chemistry textbook, writes that "the chemist's equation is a kind of equation of second rank, and the first-rank equation is the equation of the physicist." [Atkins, Physical Chemistry, Oxford University Press, 1978] The remark captures the hierarchical relationship between the disciplines. Chemistry's laws are derivable from the laws of physics, though full derivation remains incomplete for complex systems, and the derivability is what makes chemistry a natural science continuous with physics. The continuity is valid and an important element. It means that there is no gap between the chemical and physical descriptions of the world, no point at which chemistry introduces entities or principles that physics does not underwrite. The continuity also means that the limitations of physics propagate upward. Whatever physics cannot explain, chemistry inherits as unexplained. The existence of atoms, the values of the physical constants that determine their properties, the quantum mechanical laws that govern their behavior are all features of the world that chemistry assumes and that physics acknowledges as primitive.
The natural sciences built upon chemistry inherit the same assumptions at greater remove.
Geology assumes chemistry assumes physics.
Atmospheric science assumes chemistry assumes physics. The sequence of assumptions is unbroken, and at its terminus lies a discipline that has identified its own starting points as unexplained. The practical success of chemistry and the natural sciences is often invoked, implicitly if not explicitly, as evidence that the existential question is either unimportant or misguided. If chemistry can synthesize new drugs, geology locate mineral deposits, and atmospheric science model climate change, then whatever remains unexplained about the ultimate foundations of the physical world seems irrelevant to the enterprise. The invocation reflects a reasonable attitude toward the practice of science. Scientists work within frameworks that produce results, and questions that do not bear on those results can reasonably be set aside in the course of daily work. The practical attitude does not, however, constitute an answer to the existential question. That chemistry works without answering the question of why there is matter to study is entirely consistent with the observation that the question remains unanswered. The success of the enterprise depends on the existence of its subject matter. The subject matter's existence is what the question asks about. The success of the enterprise in describing and manipulating what exists has no bearing on why anything exists to be described and manipulated. Hoffmann, reflecting on the philosophical dimensions of chemistry, has noted that chemists are generally comfortable with the given character of their subject matter and rarely feel the need to interrogate it. [Hoffmann, The Same and Not the Same, Columbia University Press, 1995] The comfort is understandable, and is also an instance of the broader pattern. The question is set aside because the discipline functions without it, and the setting aside is so complete that the question rarely appears within the discipline's discourse. Taken as a whole, the natural sciences describe the behavior of matter at every accessible scale, from subatomic particles through molecules, minerals, organisms, ecosystems, atmospheres, and planetary systems. The descriptions are interconnected. Each level builds on the level below, and the connections between levels have been traced with increasing precision as scientific knowledge has advanced. The interconnection is a central achievement of modern science, revealing a physical world that is unified in its operations even as it displays considerable variety in its manifestations. The unification operates entirely within existence. It connects descriptions of existing things at different scales without addressing why there are things at any scale. The inventory of what exists grows more complete and more interconnected with each advance.
The question of why there is an inventory at all persists through the advances, receiving no treatment from the disciplines that compile it. Chemistry and the natural sciences answer what matter does with a thoroughness and precision that continues to expand.
The question of why there is matter remains where it was when the investigation began.