Epigenesis is the complex process by which organisms are formed from a single cell. It is a continuation of cosmic development to produce an individual living organism, which is organised as a three-dimensional strucure of cells and organs that are discrete from the environment only so long as it is alive. When it dies it comes into chemical and energy equilibria with the cosmos. This does not mean that while alive it is cut off from its environment by an impenetrable barrier. On the contrary, it is very much dependent on its environment for its continued existence and the continually exchange matter and energy between the cosmos and itself.

It is from its environment that a living organism obtains those chemical substances needed for repair and the replacement of worn-out parts, for growth and for reproduction.

Some organisms — such as green plants — are able to use, and to accumulate the energy of sunlight, while others — such as all animals — rely on that liberated during the chemical reactions involved with the breakdown of food for all their energy needs. This energy, from whatever source, is needed to drive the chemical reactions of building, as well as for movement and the transport of chemicals within the organism, and between it and its environment, across the intervening boundaries of cells and the body.

The basic unit of which living organisms are composed is the cell, a structure typically only micrometres in diameter yet capable of carrying out the most elaborate chemical processes. The simplest organisms living independently of others are the bacteria, but their cells are less complex than those of the simplest plants and animals.

The most complex plants and animals are composed of many millions of cells and these are differentiated into a number of cell types concerned with particular functions.

Living organisms generally respond to environmental stresses in ways which prolong their survival. Thus, for example, green plants grow towards the light, and animals move away from extremes of heat and cold. In many cases these responses are built into the nature of the organism; in others they are acquired as the result of interactions with the environment itself (nurture).

The constancy of the nature of different types of organism is due to heredity, and is a consequence of the precise replication of large chemical molecules —the nucleic acids - which encode the instructions for the organism's development and activities in the DNA chains comprising genes.

The nurture of an organism not only has a direct effect on the expression of its heredity but also causes it to become better adapted to its environment. Variation in the heredity of related organisms results in some being better able to respond to environmental stresses and these organisms are more likely to survive and to become the parents of the next generation of individuals (natural selection).

Progressive adaptation of the genes through natural selection, with its concomitant elaboration of structure and function, results in the evolution of new kinds of individuals. It is in this way that the great diversity of living organisms have originated from much more simply organised ancestors over the millions of years that life has existed on this planet.

This theme may be developed by an account of the chemical composition of living organisms, with descriptions of cell structure and accounts of the simplest forms of free-living organisms, the viruses, bacteria and blue-green algae. The bioichemical aspects include an account of the synthesis of proteins, and the formation of ATP, the energy currency of all living organisms. This leads to a study of the nutrition in plants, animals and other living organisms, and use to which the assimilated food is put in the process of growth, reproduction and development.

Development of an individual from a single cell involves an increase in cell number and the subsequent differentiation of the primary cell mass, that is, functional specialisation of first cells. At first, the difference between the cells is not great and regeneration of the whole embryo from a part can occur, but, as development proceeds and the embryonic tissues differentiate into adult tissues, this power of regeneration is progressively lost. Thus, during the development of their offspring the characteristics of the parents represented in the gametes by replicates of their DNA molecules are progressively expressed. Our knowledge of the processes involved in this cellular differentiation is at present incomplete and speculative since it is based on a small number of observations in a restricted number of different organisms.

In complex organisms, an embryo develops from the fertilised primary cell (zygote or spore) as the result of a series of mitotic cell divisions. Although all the cells of an organism formed in this way contain identical complements of genes, during development morphological and physiological changes take place in these clonal cells which result in the development of the many cell types characteristic of plants and animals.

For example, the sea urchin zygote has a characteristic band of pigmented granules in the cortex just below the equator. The position of this definite band has enabled embryologists to follow the distribution of the different regions of the egg as the embryo develops. The first division of the fertilised egg (cleavage) passes through both poles of, described as the animal and vegetal poles, and divides the egg into equal halves. The second cleavage is at right angles to the first and also passes through the animal and vegetal poles and divides the egg into equal quarters. The third is at right angles to the first and the second in the horizontal plane just above the equator. The embryo at this stage consists of four similar smaller cells called mesomeres in the animal half and four similar larger macromeres in the vegetal half. The inequality of the third cleavage is due to the presence of more yolk in the vegetal half than in the animal half. Yolk tends to impede cleavage. The greater amount of yolk in an amphibian egg impedes cleavage in the vegetal region to an even greater extent, and in reptilian and bird eggs, where the amount of yolk is vast, there is no cleavage at all in the vegetal region.

If a cell nucleus is planted into an egg from which the nucleus has been removed (enucleate),of the same species, normal embryos are produced, except when damage is caused to the donor nucleus or recipient cytoplasm. In experimental work of any kind, but particularly in biology where there are so many unknown variables, it is absolutely essential to have controls which are identical with the experimental individuals in every way except that being investigated.

When a nucleus is taken from a hybrid frog embryo formed in this way and put back, as it were, into an enucleate egg of another species, an embryo is formed, but it is not viable. This shows that the cytoplasm has had an effect on the nucleus. It is also clear from such experiments that the cytoplasm is not inert with regard to development. If it were inert, any nucleus would function when in a foreign cytoplasm. If the cytoplasm of the egg of a particular species were the same as that of a the donor egg one would expect an egg containing a successfully transplanted nucleus from another species would develop into a donor individual, but it does not.

A large number of the failures are known to be due to faulty experimental technique, and to imperfect replication of the donor nucleus. The proportion of nuclei giving normal embryos decreases as the embryos from which they are taken become more differentiated. This shows there is a progressive loss of potency of cells to take over the control of normal development. These experiments also show there is no selective permanent inactivation of genes as differentiation throughout development proceeds. Specialisation involves the differential activity of genes present in every cell of the organism.

Further discussion of cellular differentiation requires some information about the mechanism of gene action because not all genes are active at the same time in different cells, and consequently, the characteristics of different tissues are due to the activity of certain genes or groups of genes which are switched on.

The switching on of genes has been extensively studied in microorganisms. A culture of the bacterium E. coli adapted to a medium containing glucose as its carbon source will grow rapidly if the glucose and other substances required for growth are present in optimal amounts. If the bacterial cells are separated from the medium, to avoid damaging the cells, and the nutrient medium is replaced by one containing lactose instead of glucose, there will result an immediate cessation of population growth because the cells are unable to utilise the new substrate. However, after a short interval, growth will resume. During the delay period genes are switched on to form the mechanisms to utilise lactose.

In more complex organisms cellular specialisation and embryonic differentiation are very precise processes. Development proceeds along definite pathways, with forks controlled by switch mechanisms, at which differentiation occurs. The presumptive areas of the embryo differentiate into the basic tissues which then undergo further and further differentiation until the adult tissues are formed.

Regulation of the formation of organs systems that define a species requires that the genotype should remain unchanged from generation to generation. In biochemical terms, we mean that the proteins determined by the genotype's constituent codes should have an invariable amino acid composition. This is only possible if the coding mechanism is essentially conservative and resistant to environmentally induced changes.

Nevertheless, in some instances it is advantageous for an organism to conform to a stress. Galactosidase induction in Escherichia coli is an example of this. When an organism does conform it is better that it should do so in an optimal way rather than in a variable one. When this bacterium is placed in an environment containing a new food medium it is advantageous that it should produce the appropriate enzyme in the correct quantity for optimum substrate utilisation. Those variant bacteria which can do this best will be more likely to survive, grow and multiply than the others. Should a genetic change in the mechanism controlling enzyme activity resulting in optimal substrate usage occur in these selected bacteria, it will be immediately assimilated into the genetic system of the population because of its advantage to the individuals possessing it.

In higher organisms, genetic adaptations to changes environment through natural selection begin by variations in embryonic development that may result, for example, in a slightly larger beak, a faster or slower rate of growth.

Ageing is a continuation of the processes of development. These changes result from the accumulation of errors in the workings of genes that eventually result in the organism being unable to adapt to environmental stress.

The cellular controls of epigenesis are expressed at the level of size and shape of cell populations. In this sense evolution is limited by what has already been selected in terms of the forms and organ structures generated during the process of epigenesis. Emergent order is generated by distinctive types of dynamic process in which genes play a significant but limited role. Epigenesis as a process is the source of emergent evolutionary properties, and it is the absence of a theory of organisms that includes this basic generative process that has resulted in the failure to account for the origin of the emergent characteristics that identify species.

Many people have recognized this limitation of Darwin's vision. It was the achievement of D'Arcy Thompson in his volumes On Growth and Form (1917) in which he single-handedly defines the problem of biological form in mathematical terms and re- establishes the organism as the dynamic vehicle of biological emergence. Once this is included in an extended view of the living process, the focus shifts from inheritance and natural selection to what Brian Goodwin has described as creative emergence of high level structures as the central quality of the evolutionary process. And, since organisms are primary loci of this distinctive quality of life, they become again the fundamental units of life, as they were for Darwin. Inheritance and natural selection continue to play significant roles in this expanded biology, but they become parts of a more comprehensive dynamical theory of life which is focused on the dynamics of emergent processes.

According to Goodwin, the consequences of this altered perspective are considerable, particularly in relation to the status of organisms, their creative potential, and the qualities of life. Organisms cease to be simply survival machines and assume intrinsic value, having worth in and of themselves, like works of art. Such a realization arises from an altered understanding of the nature of organisms as centres of autonomous action and creativity, connected with a causal agency that cannot be described as mechanical. It is relational order between components that matters more than material composition in living processes, so that emergent qualities predominate over quantities. This consequence extends to social structure, where relationships, creativity and values are of primary significance. As a result, values enter fundamentally into the appreciation of the nature of life and biology takes on the properties of a science of qualities. This is not in conflict with the predominant science - of quantities - but it does have a different focus and emphasis.

Darwinism sees the living process in terms that emphasize competition, inheritance, selfishness, and survival as the driving forces of evolution. These are certainly aspects of the remarkable drama that includes our own history as a species. But it is a very incomplete and limited story, both scientifically and metaphorically, based upon an inadequate view of organisms; and it invites us to act in a limited way as an evolved species in relation to our environment, which includes other cultures and species. These limitations have contributed to some of the difficulties we now face, such as the crises of environmental deterioration, pollution, decreasing standards of health and quality of life, and loss of communal values. But Darwinism short-changes us as regards our biological natures. We are every bit as co-operative as we are competitive; as altruistic as we are selfish; as creative and playful as we are destructive and repetitive. And we are biologically grounded in relationships which operate at all the different levels of our beings as the basis of our natures as agents of creative evolutionary emergence, a property we share with all other species. These are not romantic yearnings and Utopian ideals. They arise from a rethinking of our biological natures that is emerging from the sciences of complexity and is leading towards a science of qualities which may help in our efforts to reach a more balanced relationship with the other members of our planetary society.