This chapter establishes the conceptual approach that will be used for the exploration of cancer and presents background material that will used throughout.

Section 1 - Persistent Patterns

This section opens with a discussion of various historical and philosophical approaches to sorting out the complexities of the living world, which serves as a prelude to the establishment of a conceptual approach that avoids idealistic distinctions (e.g. species) and the imposing of patterns upon nature in favour of allowing natural patterns to emerge on their own merits. With that basic approach established, the process of assembling a conceptual model of the living world begins with a consideration of how we recognize living things from their interaction with their surroundings and each other. That conceptual model emphasizes the connections that run throughout the living world, beginning with the inorganic elements, energy and molecules that are continually incorporated into the organic realm in the form of biomolecules which serve as fuel and building blocks for the assembly of the more complex structures - such as macromolecules and cells - that are associated with the growth, development and regeneration of all living creatures. These continual throughputs of matter, energy and molecular complexity link living things to each other in a variety of ways, and those connections can be used as a starting point for recognizing patterns within the living world, such as natural communities.

Section 2: Emergent Organizations

This section opens with a discussion of how we can recognize communities of living things on their own merits, and the first key to doing this comes from the observation that some communities are not only easy to recognize by their physical presence on the landscape, they also interact with their surroundings as communities rather than as collections of individual creatures. The primary example discussed is that of tropical rainforests, which are not only easy to pick out as the world's largest, densest and most diverse living communities, but their ability to remain large, dense and diverse depends upon large-scale environmental interactions such as the "rain recycling pump" that allows large, dense forests to pass moisture much farther along than it would travel over open ground (which is why the deforestation of coastal regions can contribute to the expansion of deserts farther inland). In order to participate in such an interaction a forest community must achieve and maintain a certain size and density, hence the interaction is an example of an emergent characteristic. Such characteristics allow us to recognize communities and other kinds of living organizations on their own merits, and they also provide a starting point for recognizing differences among various kinds of organizations. For instance rainforest communities tend to maintain consistent internal environments and so do many of the creatures living within them, but forests do not possess the elaborate physiological and behavioural adaptations that organisms use to regulate internal conditions. The development of communities and creatures is also quite different, since complex organisms develop in highly controlled environments according to precise timetables that are strongly influenced by hereditary information, while the development of living communities proceeds in a much more ad hoc manner with highly variable results.

These differences between communities and organisms may seem obvious, but they have not always been so to biologists, including the early 20th century ecologists who developed the concepts of the superorganism and the ecosystem, both of which are discussed and rejected in favour of a simpler and more flexible conception of living communities. That flexibility begs the question of how far the concept of a living community can be extended, and the logical place to start such an examination is with the concept of Gaia - specifically Lovelock's most restrained depiction of Gaia as a global supercommunity which may possess certain emergent properties in relation to its interactions with the planetary environment. Those interactions are considered first from the perspective of space, via comparisons of the planetary bodies within our solar system, among which the Earth clearly stands out as being in a state of chemical disequilibrium; for instance we have an enormous amount of oxygen in the atmosphere. The development of this unique situation is then considered from a historical perspective, beginning at a time when our planet was in chemical equilibrium and retracing the emergence of a non-equilibrium state via the interaction of cells and cellular communities with each other and their environments.

The story continues with the emergence of multicellular creatures, the appearance life on land and the various physical and biological events (e.g. mass extinctions) that contributed to the emergence of the biosphere we are familiar with today. In the end we have a story that provides a conceptual framework for thinking about the living world as having a lengthy history and incorporating interactions that involve very large scales of time and space. The question of whether the living world, the biosphere or Gaia can be considered to maintain homeostasis or possess something like a physiology is explored but left open to serve as an introduction to an examination of living things that definitely do possess such characteristics.

Section 3 - Informed Organizations

This section deals with the kinds of living organizations that most of us have no difficulty in recognizing, the organisms. Following the established approach the first step towards sorting organisms is to see how they sort themselves, and here one of the most obvious distinctions involves lineages: cells come from cells, roses come from roses, horses come from horses, people come from people. The concept of the species is rejected as an idealistic designation that has little relevance to what goes on in the living world, where what we actually find are families, breeding populations and lineages that can be distinguished by the information they share and perpetuate. The relationships among lineages can be used to construct a systematic classification system where unlike the traditional taxonomic system the distinctions are provisional - for instance the relationships among lineages can be rearranged on the basis of DNA analysis - and not necessarily absolute; for example it is possible for distantly related lineages to exchange DNA on occasion.

With these basics established the next step is to sort out what kinds of information organisms share and perpetuate and how they interact with that information. For instance organisms like us are capable of acquiring and passing on cultural information as well as the hereditary information that is embodied in eggs and sperm, which is also passed on when cells divide within our bodies. These observations serve as a lead-in to a discussion of various theories concerning how information is associated with the form and development of organisms, which serves as a prelude to an examination of the embryonic development of complex organisms, or epigenesis. That examination begins with an excursion into the realm of viruses, whose life cycles illustrate the roles played by the basic components of the cellular information-handling machinery (e.g. DNA, RNA, ribosomes, enzymes, etc.), as well as the importance of processes like macromolecular self-assembly. With these basics established the examination moves on to consider what happens during epigenesis by considering some standard examples (e.g. fruit flies, frogs and chickens) that are used to establishing key concepts such as cell differentiation and regeneration, which are critical to the understanding of cellular cancers. The point is made that while epigenesis appears to be a highly deterministic process, the patterns it produces are not predetermined but emergent, which has some important implications for how things can change in the living world.

Section 4 - Patterns of Change

This section is concerned with the one thing that is inescapable for everything in the living world, from Gaia to the tiniest cell: change. There are many ways of appreciating how living things change, with the most extreme position being that most of the variations we observe are irrelevant. For instance according to Aristotle the evolutionary journeys of individuals may vary - for instance a seed that falls on rock will not germinate and a trampled seedling will not become a tree - but the ultimate goal never changes and thus the forms of organisms cannot change over time. Of course Aristotle did not know about DNA, and once we recognize the role of hereditary information in the living world the picture changes completely. For instance not only do genomic lineages continually accumulate changes due to replication errors and mutational damage, but many organisms deliberately introduce random genomic changes during reproduction, ensuring the continual creation of new variations.

The recognition of the inevitability of change and the prominent role played by chance serves as the lead-in to a discussion of the kinds of changes that can appear in the living world, their consequences and contexts. For instance when populations or lineages lose reproductive contact with each other their genomic information naturally tends to diverge, and such divergences can lead to the emergence of physical and/or behavioural differences among populations and lineages. Such variations can also emerge within lineages and populations, and if those variations affect survival and reproductive success they can become involved in what is commonly called Darwinian evolution - a subject that is discussed at some length with regards to evolutionary changes in lineages, populations, genomes, living communities and ultimately the entire biosphere. For instance the periods following mass extinctions have been marked by the emergence of new kinds of natural communities worldwide and with rapid and radical changes within many organism lineages, such as the explosion in new varieties of mammals following the K-T debacle.

By the end of the chapter the major concepts of variety, change, organization, information, evolution and survival are combined in a vision of the living world that is markedly different from the traditional conception of a planet with a place for everything and everything in its place, set within a universe that is proceeding grandly towards perfection. Instead we find a world full of lineages, populations, communities and other participants in the ongoing struggle to survive and contribute to posterity, all of which are involved in evolutionary journeys where chance plays a major role but not predetermined goals, external guidance or ideal models. Some routes may seem easier to follow than others and some destinations may seem quite attractive, but a close look at each journey inevitably reveals not a smooth and irresistible progression but a series of small and short-sighted steps - the kinds of steps that can lead towards destinations that would make no sense in a perfect world.