Information and Genetics

I don't know if this has been covered recently or not, but what information does DNA really convey?I am involved in microbiology and molecular biology and know from experience that it is very difficult to know what a gene does without studying the protein it codes for. It is difficult to look at the DNA sequence and to calculate substrate specificity, enzymatic effeciency, pH optimums, oxygen lability, temperature optimum, oligimerisation (sp?), and so forth. As far as I can see, the only real information a DNA sequence conveys is in the activity of the protein it codes for. In general, mutations in the DNA sequence may or may not affect protein effeciency or specificity. You can theorize if site specific mutations will cause an effect, but working with the protein is the only way to test the theory. Also, wouldn't different DNA sequences "mean" the same thing if they produce proteins that do the same thing?In practice, genetic sequences are often given hypothetical designations due to their genetic homology to other gene sequences. For instance, you can look at a sequence and say with high probability that it codes for a polymerase because it has 98% homology to another polymerase. However, the activities of the homolog were only discovered by observing the protein. Protein motifs (helix-helix turns and so forth) are treated in the same way. Amino acid sequences (motifs) are compared to known activies/structures derived from observing the protein.As a thought experiment, if you were to randomly assemble a 4 kb DNA sequence without internal stops (i.e., an open reading frame with a promoter) could you deduce the activity of the protein produced, if it is active at all? And if you don't know what the protein does, what information does the DNA sequence convey?Sorry if this is going over heavily trodden territory, but these thoughts just kept coming to me when reading this thread. Those, and how TATTA boxes always make gene jockeys snicker like school boys.

Good point Rei. I believe someone els brought a similar point as well, that is many people look at the replication of DNA as a complex chemical reaction, which it is.Taking this a little further, could we say that the orbitals of atoms carry coded information since they code for certain chemical reactions. Why not Na2Cl instead of NaCl? Because the reaction was derived from the coding in the orbitals. There we are, non biological coding system, simple atomic orbitals.It has semantics (haven't done it since college chem, but 1d and 2e seem familiar) in that the orbitals have rules and syntax that allow them to combine in precise fashion.It has been some time since college chem, but wouldn't atomic orbitals fall under the umbrella of a non-biological coding system that occurs naturally?