In which we consider what biology is all about, namely organisms and their diversity. We discover that organisms are built of one or more, sometimes many cells that act in a coordinated (social) manner. We consider the origins of organisms, their basic properties, and their relationships to one another.
Biology is the science of organisms, how organisms function, behave, interact, adapt, and, as populations, have and can evolve. As we will see, organisms are discrete, highly organized, bounded but open, non-equilibrium, physicochemical systems. Now that is a lot of words, so the question is what do they mean? How is a rock different from a mushroom that looks like a rock? What exactly, for example, is a bounded, non-equilibrium system? The answers are not simple; they assume a working knowledge of thermodynamics, a complex topic that we address in Chapter 5. For the moment, when we talk about a non-equilibrium system, we mean a system that can do various forms of work. Of course that means we have to define what we mean by work. For simplicity, we will start by defining work as some outcome that takes the input of energy to achieve. In the context of biological systems, work ranges from generating and maintaining molecular gradients and driving other unfavorable, that is energy-requiring reactions, such as the synthesis of a wide range of biomolecules, including nucleic acids, proteins, lipids, and carbohydrates, required for growth, reproduction, the generation of movement, and so on.
We will focus on what is known as free energy, which is energy available to make things happen. When a system is at equilibrium, its free energy is 0, which means that there are no macroscopic (visible) or net changes. The system is essentially static, even though at the molecular level there are still movements due to the presence of heat. Organisms maintain their non-equilibrium state (their free energy is much greater than zero) by importing energy in various forms form the external world. Organisms are different from other non-equilibrium systems in that they contain a genetic (heritable) component. While other types of non-equilibrium systems occur in nature – hurricanes and tornados are non-equilibrium systems – they differ from organisms in that they are transient. They arise de novo and when they dissipate they leave no offspring, no baby hurricanes. In contrast, each organism alive today arose from one or more pre-existing organisms (its parent(s)) and each organism, with some special exceptions, has the ability to produce offspring. As we see, the available evidence indicates that each and every organism, past, present, and future, has (or will have) an uninterrupted history stretching back billions of years. This is a remarkable conclusion, given the obvious fragility of life, and makes organisms unique among physiochemical systems.
Biology has only a few over arching theories. One of these, the Cell Theory of Life, explains the historic continuity of organisms, while the Theory of Evolution by Natural Selection (and other processes), explains both the diversity of organisms and how populations of organisms can change over time. Finally, the Physicochemical Theory of Life explains how it is that organisms can display their remarkable properties without violating the laws that govern all physical and chemical systems.