For most of the twentieth century, biologists have been somewhat uneasy about Darwin's theory of evolution. No one doubted the fact of evolution, but the mechanism of evolution was obscure. This was apparently because biologists were looking for a linear explanation of a non-linear system, and they were searching at too low a systems level.

It was usually argued that the mechanism of evolution was natural selection operating on random mutations. However, this postulated mechanism presents insuperable problems. Random mutations occur in individuals, and this mechanism would allow natural selection to occur only at the systems level of the individual. Group selection would be impossible. Furthermore, random mutations are rather rare, and they are usually detrimental.

Darwin thought primarily in terms of natural selection operating on differences in morphology. Later, differences in behaviour were also emphasised. Stewart Kauffman (1993) took this idea even further with his proposal that the mechanism of evolution is natural selection operating on self-organisation. We may conclude eventually that the mechanism of evolution is natural selection operating on emergents, at all systems levels. Only the systems with the fittest emergents survive. With this conclusion, all problems concerning the mechanism of evolution seem to disappear. This is a non-linear explanation of a non-linear system. It is also Wolfram's (2002) 'new kind of science' in which simple causes produce complexity, in the manner of cellular automata.

By analogy, we can compare Darwinian evolution with the growth of a great literature. Each new book is the equivalent of a new species. It survives or disappears on the basis of its quality. This quality is an emergent. As better and better books appear, the inferior works tend to be forgotten. The growth of literature is the result of selection operating on the book qualities, the emergents. To postulate that Darwinian evolution is the result of random mutations is rather like suggesting that the growth of literature is the result of printing errors. And to postulate that there can be millions of mutations over millions of years does not really help. Darwinian evolution is an increase in the complexity of pattern, and this increase occurs because all living systems are both open systems and complex adaptive systems, that have the property of self-organisation. And this argument applies at all systems levels, from the DNA, to the chromosome, the cell, the organism, the population, the ecosystem, and the biosphere. Books, on the other hand, are simple static systems. They cannot self-organise, but they can be read, and the reaction of innumerable readers does lead to self-organisation, which decides the survival or extinction of individual books.

These arguments become crucial in our consideration of the evolution of the vertical subsystem, and the n/2 model (see 4.15). When considering the evolution of the gene-for-gene relationship, it is impossible to think in terms of the separate evolution of the host and the parasite. We must consider their combined evolution, as a single system. And we must think of this evolution being natural selection operating on the emergents of the single system, at the level of the pathosystem. That is, at the systems level of the two interacting populations of host and parasite. It will be demonstrated later (see 4.20) that the evolution of the gene-forgene relationship and the vertical subsystem is impossible if selection can occur only at the level of the individual. But gene-for-gene relationships have evolved, many times, in many widely diverse plant hosts, and in many different parasites, ranging from nematodes and insects, through parasitic Angiosperms to fungi, bacteria, and viruses. Consequently, we are compelled to conclude that natural selection operating on random mutations is not the sole, or even the main, mechanism of Darwinian evolution.

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