If, in some cataclysm, all of scientific knowledge were to be destroyed, and only one sentence passed on to the next generation of creatures, what statement would contain the most information in the fewest words? I believe it is the atomic hypothesis (or the atomic fact, or whatever you wish to call it) that all things are made of atoms—little particles that move around in perpetual motion, attracting each other when they are a little distance apart, but repelling on being squeezed into one another. In that one sentence, you will see, there is an enormous amount of information about the world, if just a little imagination and thinking are applied.  – Nobel Laureate Richard Feynman, 1963

Most of us are quite familiar with the core principle of atomic theory—the idea that matter is composed of atoms—because we have been told that this is so since childhood. But how many of us really, and we mean really believe it, use it in our day-to-day life, understand its implications, or know the reasons why it is assumed to be true? It seems so completely and totally impossible and improbable because we do not experience atoms directly and it is easy to go through life quite successfully, at least for the vast majority of us, without having to take atoms seriously. The average person’s brain is simply not wired to believe in the reality of things like atoms in a concrete and day-to-day way. Yet most scientists, and certainly most chemists, would agree that Feynman’s deceptively simple statement contains the essence of chemistry.

Atomic theory is also critical for understanding a significant number of the underlying concepts of biology and physics, not to mention geology, astronomy, ecology, and engineering. How can one sentence contain so much information? Can we really explain such a vast and diverse set of scientific observations with so little to go on? In the next chapters we will expand on Feynman’s sentence to see just what you can do with a little imagination and thinking. At the same time, it is worth remembering that the fact that atoms are so unreal from the perspective of our day-to-day experience means that the atomic theory poses a serious barrier to understanding modern chemistry. This is a barrier that can only be dealt with if you recognize it explicitly and try to address and adjust to it. You will be rewiring your brain in order to take atoms, and their implications, seriously. We are aware that this is not an easy task. It takes effort, and much of this effort will involve self-reflection, problem-solving, and question-answering. In an important sense, you do not have to believe in atoms, but you do have to understand them.

What Do You Think You Know About Atoms?

You almost certainly have heard about atoms and it is very likely you have been taught about them. If asked you might profess to believe in their reality. You might accept that matter, in all its forms, is made up of atoms — particles that are the smallest entities that retain the identity of an element (we will discuss elements in much greater detail in the next few chapters.) It is very likely that you have been taught that atoms are made up of even smaller particles: positively charged protons, uncharged neutrons, and negatively charged electrons. You may even have heard, and perhaps even believe, that protons and neutrons can be further subdivided into quarks and gluons, while electrons are indivisible. Equally difficult to appreciate is that all atoms are organized in a very similar way, with a very tiny, but relatively heavy, positively charged nucleus surrounded by the much lighter, negatively charged electrons.

Part of the difficulty in really understanding atoms is the fact that the forces holding the atomic nucleus together, the so-called strong and weak forces, operate at such infinitesimal distances that we do not experience them directly. This is in contrast to electromagnetism and gravity, which we experience directly because they act over longer, macroscopic or visible distances. A second problem is associated with the fact that to experience the world we need to use energy; at the atomic scale the energy used to observe the system also perturbs it. This is the basis of the Heisenberg uncertainty principle, which you may have encountered or at least heard of before, and to which we will return. Finally, objects at the atomic and subatomic scales behave differently from the macroscopic objects with which we typically interact. A particle of light, a photon, an electron, a proton, or a neutron each behaves as both a particle and a wave. In terms of physics, these are neither particles nor waves; they are quantum mechanical particles. Luckily, the weirder behaviors of atomic and subatomic entities can often, but not always, be ignored in chemical and biological systems. We will touch on these topics as necessary.

Current theory holds that each atom contains a very, very small, but very dense nucleus, which contains protons and neutrons and is surrounded by electrons. These electrons are very light, relatively, but the space occupied by moving electrons accounts for the vast majority of the volume of an atom. Because the number of positively charged protons and negatively charged electrons are equal and the size of the charges are the same but opposite, atoms are electrically neutral when taken as a whole; that is, each positively-charged proton is counterbalanced by a negatively-charged electron.

Often the definition of an atom contains some language about how atoms are the smallest particle identifiable as that element. What do we mean by that? For example, can an atom have chemical properties? And how can ensembles of the same particles, that is protons, electrons, and neutrons, have different properties? This is the mystery of the atom and understanding it is the foundation of chemistry. Here, we hope to lead you to a basic understanding of atomic structure and inter-atomic interactions. Subsequent chapters will extend and deepen this understanding.

Atomic Realities and Scientific Theories

We assume that you have lots of ideas about atoms but did you ever stop to think how we came to accept this information as reasonable or what the reality of atoms implies about how the world we perceive behaves? Atoms are incredibly and unimaginably small. A gold atom with its full complement of electrons is less than a nanometer (1 x 10^–9 meters) in diameter and its nucleus, which contains 79 protons and generally around 116 neutrons, has a radius of ~1.5 x 10^–14 meters. While these sizes are actually unimaginable, there are a number of web-based activities that can help you come to terms with the scales of atoms.^[1] There is no way you could see an atom with your eye or with a light microscope, although there are now techniques that allow us to view computer representations of individual atoms using various types of electron and force-probe microscopes. The smallest particle of matter that you can see with your naked eye contains more atoms than there are people in the world. Every cell in your body contains a huge number of atoms. Obviously, whatever we know about atoms is based on indirect evidence; we do not directly experience atoms.

The full story of how we know what we know about the existence and structure of atoms is fascinating, complex, and perhaps fortunately for you, too long to go into in detail. What we do want to do is to consider a number of key points that illustrate how our ideas of atoms arose and have changed over time. We will present the evidence that has made accepting the atomic theory unavoidable if you want to explain and manipulate chemical reactions and the behavior of matter.

Atomic theory is an example of a scientific theory that began as speculation and, through the constraints provided by careful observation, experimentation, and logical consistency, evolved over time into a detailed set of ideas that make accurate predictions and are able to explain an increasing number of diverse, and often previously unknown, phenomena. As scientists made new observations, atomic theory was adapted to accommodate and organize these observations.

A key feature of scientific ideas, as opposed to other types of ideas, is not whether they are right or wrong but whether they are logically coherent and make unambiguous, observable, and generally quantitative predictions. They tell us what to look for and predict what we will find if we look at or measure it. When we look, we may find the world acts as predicted or that something different occurs. If the world is different from what our scientific ideas suggest then we assume we are missing something important: either our ideas need altering or perhaps we are not looking at the world in the right way. As we will see, the types of observations and experimental evidence about matter have become increasingly accurate, complex, and often abstract, that is, not part of our immediate experience. Some of these observations can be quite difficult to understand, because matter behaves quite differently on the atomic and sub-atomic scale than it does in the normal, macroscopic world. It is the macroscopic world that evolutionary processes have adapted us to understand, or at least cope with, and with which we are familiar. Yet, if we are to be scientific, we have to go where the data lead us. If we obtain results that are not consistent with our intuitions and current theories, we have to revise those theories rather than ignore the data.

However, scientists tend to be conservative when it comes to revising well-established theories because new data can sometimes be misleading. This is one reason there is so much emphasis placed on reproducibility. A single report, no matter how careful it appears, can be wrong or misinterpreted and the ability of other scientists to reproduce the observation or experiment is key to its acceptance. This is why there are no miracles in science. Even so, the meaning of an observation is not always obvious or unambiguous; more often than not an observation that at first appears to be revolutionary turns out to have a simple and even boring explanation. Truly revolutionary observations are few and far between. This is one reason that the Carl Sagan (1934-1996) quote, “Extraordinary claims require extraordinary evidence” is so often quoted by scientists. In most cases where revolutionary data is reported, subsequent studies reveal that the results were due to poor experimental design, sloppiness, or some irrelevant factor. The fact that we do not all have cold fusion energy plants driving perpetual motion refrigerators in our homes is evidence that adopting a skeptical approach that waits for experimental confirmation is wise.

A common misconception about scientific theories is that they are simply ideas that someone came up with on the spur of the moment. In everyday use, the word theory may well mean an idea or even a guess, a hypothesis, or a working assumption, but in science the word theory is reserved for explanations that encompass and explain a broad range of observations. More than just an explanation, a theory must be well tested and make clear predictions relating to new observations or experiments. For example, the theory of evolution predicted that the fossil record would show evidence for animals that share many of the features of modern humans. This was a prediction made before any such fossils were found; many fossils of human-like organisms have since been and continue to be discovered. Based on these discoveries, and on comparative analyses of the structure of organisms, it is possible to propose plausible family trees, known as phylogenies, connecting different types of organisms. Modern molecular genetics methods, particularly genome (DNA) sequencing, have confirmed these predictions and produced strong experimental support for the current view that all organisms now living on Earth are part of the same family–that is, they share a common ancestor that lived billions of years ago. The theory of evolution also predicts that the older the rocks, the more different the fossilized organisms found will be from modern organisms. In rocks dated to ~410 million years ago, we find fossils of various types of fish but not the fish that exist today. We do not find evidence of humans from that period; there are, in fact, no mammals, no reptiles, no insects, and no birds.

A scientific theory is also said to be falsifiable, which doesn’t mean that it is false but rather that it may be proven false by experimentation or observation. For example, it would be difficult to reconcile the current theory of evolution with the discovery of fossil rabbits from rocks older than 300 million years. Similarly, the atomic theory would require some serious revision if someone discovered an element that did not fit into the periodic table; the laws of thermodynamics would have to be reconsidered if someone developed a successful perpetual motion machine. A theory that can be too easily adapted to any new evidence has no real scientific value.

A second foundational premise of science is that all theories are restricted to natural phenomena; that is, phenomena that can be observed and measured, either directly or indirectly. Explanations that invoke the supernatural or the totally subjective are by definition not scientific, because there is no imaginable experiment that could be done that might provide evidence one way or another for their validity. In an important sense, it does not matter whether these supernatural explanations are true or not; they remain unscientific. Imagine an instrument that could detect the presence of angels. If such an instrument could be built, angels could be studied scientifically; their numbers and movements could be tracked and their structure and behaviors analyzed; it might even be possible to predict or control their behavior. Thus, they would cease to be supernatural and would become just another part of the natural world. Given these admitted arbitrary limitations on science as a discipline and an enterprise, it is rather surprising how well science works in explaining (and enabling us to manipulate) the world around us. At the same time, science has essentially nothing to say about the meaning of the world around us, although it is often difficult not to speculate on meaning based on current scientific ideas. Given that all theories are tentative, and may be revised or abandoned, perhaps it is wise not to use scientific ideas to decide what is good or bad, in any moral sense.

As we will see, the history of atomic theory is rife with examples of one theory being found to be inadequate, at which point it must be revised, extended, and occasionally totally replaced by a newer theory that provides testable explanations for both old and new experimental evidence. This does not mean that the original theory was necessarily completely false but rather that it was unable to fully capture the observable universe or to accurately predict newer observations. Older theories are generally subsumed as newer ones emerge; in fact, the newer theory must explain everything explained by the older one and more.

Some History of Atomic Theory

Modern atomic theories have their roots in the thinking of ancient peoples, in particular ancient Greek philosophers who lived over 2500 years ago. At that time the cultural, economic, and intellectual climate in Ancient Greece permitted a huge surge of philosophical and scientific development, the so-called Greek miracle. While most people of that time believed that the world was ruled by a cohort of semi-rational gods a series of philosophers, beginning with Thales of Miletus (died 546 bce),^[2] were intent on developing rational and non-supernatural explanations for observable phenomena such as what we are made of and where we came from. As we know now, they could not possibly have understood the underlying nature of matter because they lacked the tools to observe and experiment at the atomic scale. However, this does not mean that their ideas were simple idle speculation. The ideas they produced, although not scientific as we understand the term today, contained remarkable insights – some of which appear to be true.

This era gave birth to a new way to approach and explore natural phenomena in order to gain understanding of their complexity and diversity in terms of natural explanations. It is worth considering that such a rational approach did not necessarily have to be productive; it could be that the world is really a totally irrational, erratic, and non-mechanistic place, constantly manipulated by supernatural forces; but given that science can not address these kinds of ideas, let us just leave them to fantasy authors. The assumption that the world is ruled solely by natural forces has been remarkably productive; that is, consistent with the way the world appears to behave when we look at it dispassionately.

The ancient Greeks developed complex ideas about the nature of the universe and the matter from which it was composed, some of which were accepted for a long time. However, in response to more careful observation and experimental analysis, these ideas were eventually superseded by more evidence-based theories. In large part this involved a process by which people took old ideas seriously, and tried to explain and manipulate the world based on them. When their observations and manipulations failed to produce the expected or desired outcomes, such as turning base metals into gold, curing diseases, or evading death altogether, they were more or less forced to revise their ideas, often abandoning older ideas for newer ideas that seemed to work.

The development of atomic theories is intertwined with ideas about the fundamental nature of matter, not to mention the origin of the universe and its evolution. Most Greek philosophers thought that matter was composed of some set of basic elements, for example, the familiar earth, air, fire, and water. Some philosophers proposed the presence of a fifth element, known as quintessence or aether.^[3] These clearly inadequate ideas persist today as part of astrology and the signs of the Zodiac—a poor tribute to some very serious thinkers.

The original elements, that is, earth, air, fire, and water, were thought to be composed of tiny indestructible particles, called atoms by Leucippus and Democritus (who lived around 460 bce).^[4] The atoms of different elements were assumed to be of different sizes and shapes, and their shapes directly gave rise to the properties of the particular element. For example, the atoms of earth were thought to be cubic; their close packing made earth solid and difficult to move. The idea that the structure of atoms determines the observable properties of the material is one that we will return to, in a somewhat different form, time and again. Although the particulars were not correct, the basic idea turns out to be sound.

In addition to their shapes, atoms were also thought to be in constant motion, based on watching the movement of dust motes in sunlight, with nothing, or a void, between them.^[5] Many centuries later Einstein’s analysis of this type of motion, known as Brownian motion, provided strong experimental support for the physical reality of molecules, larger structures composed of atoms, and the relationship between molecular movement, temperature, and energy, which we will consider later on.

All in all the combined notions of the Greek philosophers provided a self-consistent and satisfactory basis for an explanation of the behavior of matter, as far as they could tell. The trap here is one that is very easy to fall into, namely that a satisfying explanation for a phenomenon is not necessarily true. Even if it seems to be self-consistent, useful, or comforting, an explanation is not scientific unless it makes testable, quantitative predictions. For example, it was thought that different materials were made up of different proportions of the four ancient elements. Bones were made of water, earth, and fire in the proportions 1:1:2, whereas flesh was composed of these elements in a ratio of 2:1:1.^[6] While these ideas are now considered strange, they contain a foreshadowing of the “law of multiple proportions”, which would come some 2300 years later. Some philosophers even thought that the soul was composed of atoms or that atoms themselves had a form of consciousness, two ideas that seem quite foreign to (most of) us today.

Such ideas about atoms and elements provided logical and rational, that is, non-supernatural explanations for many of the properties of matter. But the Greeks were not the only ancient people to come up with explanations for the nature of matter and its behavior. In fact, it is thought that the root of the words alchemy and chemistry is the ancient Greek word Khem, the Greek name for Egypt, where alchemy and chemistry are thought to have originated.^[7] Similar theories were being developed in India at about the same time, although it is the Greek ideas about atoms that were preserved and used by the people who eventually developed our modern atomic theories. With the passage of time ancient ideas about atoms and matter were kept alive by historians and chroniclers, in particular scholars in the Arab world. During the European Dark Ages and into medieval times, there were a few scattered revivals of ideas about atoms, but it was not until the Renaissance that the cultural and intellectual climate once again allowed the relatively free flowering of ideas. This included speculation on the nature of matter, atoms, and life. Experimental studies based on these ideas led to their revision and the eventual appearance of science, as we now know it. It is also worth remembering that this relative explosion of new ideas was occasionally and sometimes vigorously opposed by religious institutions, leading to torture, confinement, and executions.^[8]