Integrating+pattern+formation,+coding+structure+and+evolution

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 * TO DO:**

- Add links to pages where questions 1-3 are discussed.

=Integrating pattern formation, coding structure and evolution=

In CA we see spatial pattern formation which affects ecological and evolutionary processes. Higher order patterns arise by themselves and feedback on the evolution of replicators, i.e. they enslave the evolution of replicators. This is a two-way process whereby replicators interact to generate patterns which then feedback on replicators.

On the other hand we have seen that replicators have a coding structure which leads to a particular genotype-phenotype mapping landscape. In organisms there is therefore a complex transformation from a code to an organism.

These observations lead to the following questions:
 * 1) **What is the best code?** (e.g. smooth landscape?)
 * 2) Given a code, **how does evolution proceed**, i.e. what evolutionary process? In RNA, a smooth landscape is false but appears much better for the evolutionary process, i.e. redundant coding and neutral paths.
 * 3) Given an evolutionary process, what kind of code evolves? i.e. can evolution select for certain kinds of coding because properties of the landscape are not the same everywhere, i.e. select place in genotype space such that landscape has certain properties? Moreover is it true that evolutionary processes leave an **evolutionary signature**, i.e. something that does not affect the properties of a system, but is merely a signal that show it has evolved?

In te previous pages, we have already started on giving answers to questions 1 and 2. In the coming pages, we will first elaborate on the first questions a bit more, and then switch our attention to the last question.

Next: Which code is chosen?


 * References**

(CHANGELOG 2014-2015)


 * Moved this page up in the order, used to come after discussion of multiple coding.
 * Removed text:

Although evolution is mostly visualized as a process of point mutation, duplication is actually seen as one of the major factors in evolution, at least to the same extend as point mutations. The landscape metaphor however breaks down with such mutations, and also breaks down without a fixed external fitness criterion, i.e. co-evolution. Which code evolves therefore depends on evolution to a fixed or non-fixed solution: fixed target selects robust (neutral) solution, while in co-evolution there is selection for sequences where mutations have extra effect.

Here we ask: //can we generalize on these ideas by connecting//:
 * pattern formation
 * coding structure (how they do what they do, not just what they do)
 * evolution

In other words lets study **coding and coping**.

Next: Which code is chosen?