DNA is not English

What are the rules? If they are simple, you should be able to list them right here.

The analogy between the genetic code and human language is remarkable. Spoken utterances are composed of a sequence of a rather small number of unit sounds, or phonemes (represented, at least roughly, by the letters of the alphabet). The sequence of these phonemes first specifies different words, and then, through syntax, the meanings of sentences. By this system, the sequence of a small number of kinds of unit can convey an indefinitely large number of meanings. The genetic message is composed of a linear sequence of only four kinds of unit. This sequence is first translated, via the code, into a sequence of 20 kinds of amino acid. These strings of amino acids fold to form three-dimensional functional proteins. Through gene regulation, the right proteins are made at the right times and places, and an indefinite number of morphologies can be specified.Thus in both systems a linear sequence of a small number of kinds of unit can specify an indefinitely large number of outcomes. But there is one respect in which the two systems cannot usefully be compared. In language, the meanings of sentences depend on the rules of syntax. These rules are formal and logical. In contrast, the ”meaning’ of the genetic message cannot be derived by logical reasoning. Thus, although the amino acid sequence of the proteins can be simply derived from the genetic message, the way they fold up to form dimensional structures, and the chemical reactions that they catalyse, depend on complex dynamic processes determined by the laws of physics and chemistry. It does not seems possible to draw a useful comparison between the way in which meaning emerges from syntax, and that in which chemical properties emerge from the genetic code.

An example of where the DNA code can be thought of as more of an anologue rather than digital code is in transcription factor binding sites. Here the "code" is bound based on its "shape". The binding protein can recognise varients of the sequence and will bind more or less strongly and so will activate/deactivate transciption depending on the concentration of the transcription factor.

I have to disagree with Maynard Smith & Ers Szathmáry, although I do so with trepidation since i have an almost reverential respect for these two. One of the fastest growing and most important fields in molecular biology and genetics is called bio-informatics. One of the major thrusts of this field is to use a set of very high power computer programs to scan through DNA codes and do exactly what Maynard Smith & Ers Szathmáry say cannot be done: derive by logical reasoning the genetic content of that code, the gene interactions, and to some extent the structure of the encoded proteins of the DNA sequence. This is possible precisely because the DNA code does have a fairly rigorous syntax and a lot of the current work in genetics is devoted to deciphering that syntax.

Hmm... I was under the impression that you were disagreeing in a couple of other threads. Thanks for the acknowledgement.

Is there a problem with a mechanical process being irreversible?