Biochemical Communication Code Called the Standard Genetic Code

In what sense is the genetic code a code in the usual meaning of the word? If we search in a dictionary for the word 'code', we find at least two different meanings that can be applied to the case of the genetic code:

1. System for communication (binary coding of telegraph, etc.)

2. A system used for secrecy or brevity of communication.

Moreover, we find two related verbs: to encode, that is, to translate a message into a code, and to decode, that is, to extract meaning from symbols with a procedure which is in some sense the inverse of the encoding one. It is obvious that a code is a product of human intelligence and that encoding is performed with the above-defined aims, that is, for communication and, at a more sophisticated level, for communication secrecy and/or efficiency of information transmission (compression). Surely, the most prevalent man-made code, which has allowed for the cultural development of mankind, is represented by oral and written languages. Through language, the world of thoughts and the physical world are connected by means of graphical signs and/or sound phonemes. To an arbitrary sequence of letters, i.e. an arbitrary word, is assigned one or more definite meanings. A dictionary describes such a connection in a given language: it specifies the meaning of a word using words of the same language. If we trust in the external reality of the physical world, it is trivially evident that the convention giving a meaning to a word could be changed for many or all of the words in a dictionary; this is the case of a different language. We say home in English or casa in Spanish but we remain confident that both words have the same meaning. A bilingual dictionary establishes the correspondence between words in one language and the words in a different language having the same meaning. With an entry in one language we can know the meaning in the other language: a translation is performed. This is the case of the genetic code: the genetic code is a bilingual translation dictionary with a reduced set of words and meanings. One difference from the bilingual translation dictionary, which operates in the world of meanings, is that the genetic code connects two otherwise weakly interacting biochemical worlds: the world of nucleic acids, where relevant biological information is stored, and the world of proteins, the essential chemical bricks for cellular metabolism. Thus the genetic code is truly a code in the sense of communication theory: it is a set of arbitrary symbols used for the scope of communication, i.e. for information transmission. In a typical communication process (Fig. 1a) there are five main components: an information source, a transmitter which mainly for practical reasons also encodes the information, a communication channel through which the information is sent, a receiver which usually decodes the information following definite rules depending on the encoding, and an information sink. Regarding the synthesis of proteins, we can identify some of these principal components of a communication process: the information is encoded as a sequence of codons in mRNA, which are sent through the nuclear membrane for protein synthesis. This information is read by the decoder/receiver, consisting of the tRNAs and the ribosome synthesis machinery, following the rules of the genetic code. Finally, the proteins, which represent the biological meaning of the encoded message, are used for the cell metabolism: the information sink. However some pieces are missing: the information source is unknown, as it is the encoding part of the transmitter; the information is available in an already encoded format (see Fig. 1b). As a consequence, the decoding step is slightly different from usual communication systems where the information sources a)

Information

Source

Encoding & Transmission b)

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