... phenotype1
The term ``map'' contains an important limitation: In this case, I'm not looking at the process by which genotype gives rise to phenotype. In RNA, the thermodynamic equilibrium secondary structure (phenotype) can be obtained from the sequence (genotype) without knowledge of the actual folding process. A kinetic model of folding, however, would be the appropriate analogue of development as a dynamic process. 
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... individual2
An example of a mechanism that generates plasticity in higher organisms is learning, whose capacity is genetically influenced. 
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... whom3
For example, computer-representations of numbers (numerals) come in different basic shapes, such as ``integer'' or ``float''. These abstract shapes control which functions can act on these numerals. 
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... inference4
For example, a function f whose type is A (-right arrow-) B, meaning that f transforms objects of shape A into objects of shape B, can be read as a logical implication: if A, then B. The inference rule known as modus ponens states that if we are given a proof of if A, then B and a proof of A, then we can construct a proof of B. This construction corresponds to the application of f to an object g (of shape A) which yields an object h (of shape B). In the chemical metaphor it corresponds to the reaction between molecules f and g yielding h. 
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... shape5
This is less far fetched than it seems at first glance. In fact, a good chemist reads a molecular shape as a statement about the potential actions of that molecule. 
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... networks6
Many issues, however, are similar to those arising in emerging technologies, such as the peer-to-peer device control networks pioneered by Echelon Corporation, www.echelon.com. 
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... networks7
There are, of course, differences with regard to kinetics. Moreover, in molecular signaling, a communication channel is established by direct physical contact and recognition between the molecules. The number of shapes any molecular shape can recognize are limited to a few. In neural signaling, a communication channel is established by connecting two neurons with a ``wire'', and a wire can connect arbitrary neurons.