Chemical Constraint and Stereochemical Affinity
The Explanation
One possible explanation for the beginnings of biological coding is that the relationship between nucleic acids and amino acids was influenced by chemistry itself.
Under stereochemical models, particular amino acids may have had affinities for particular RNA sequences or structures. Such relationships could have provided an initial connection between the nucleotide world and the amino-acid world before the modern genetic code existed.
In this view, at least some early coding assignments need not have been arbitrary. They may have developed from molecular interactions that were available naturally.
Supporting Evidence
This explanation attempts to ground the beginning of coding in ordinary chemistry rather than assuming that a complete code appeared at once.
Experimental studies have identified some relationships between amino acids and RNA sequences or structures. Chemical interactions almost certainly influenced whatever early molecular systems preceded modern translation.
Stereochemical models therefore provide a possible natural starting point for at least some coding relationships.
Limitations
Chemical affinity has not produced a generally accepted explanation for the complete genetic code.
The modern correspondence between codons and amino acids cannot presently be derived simply from chemical necessity. Researchers therefore commonly treat stereochemical effects as one possible contributor rather than a complete explanation.
Even if chemistry favored some associations, those associations would still have to become incorporated into a dependable system of coding and translation.
Questions That Remain
How many modern codon assignments preserve traces of direct chemical relationships?
How could molecular affinity become a stable coding relationship?
How were assignments lacking an obvious stereochemical basis established?
How did primitive associations become integrated with adaptors, amino-acid charging, and translation?
Intelligent Design Response
Intelligent Design need not deny that chemical properties influenced the development of biological systems. Designed systems routinely make use of the properties of their materials.
The important question is whether chemical affinity is sufficient to explain the origin of coding or whether it accounts for only part of a larger information-processing system.
If chemical relationships explain particular associations but not the origin and coordination of the system that uses those associations, the larger explanatory question remains.