The Common Ancestor?

Wounded King has already dealt with what rRNA is. Those things are composed to varying degrees of proteins, yes, but proteins are much important for their other roles. Nearly all enzymes are proteins, and enzymes control which reactions happen when and where in the body; receptors are proteins so the way that cells respond to signals is controlled by proteins, and a lot of those signals are themselves proteins. Firstly, we were talking about molecular clocks, not constructing trees. Molecular clocks are used to date splits not construct trees.Secondly, yes, there's some similarities in the way that trees are constructed based on morphology and genetics but the genetic approach is much better because (a) genes contain much more information than morphology; (b) the identification of different characters in morphology is subjective and arbitrary whereas the identification of differences in genes is objective and consistent and (c) genes can still be reliably compared even when there is almost no morphological similarity between two organisms.A morphological comparison of Archaea, Bacteria and Eukarya would suggest Archaea and Bacteria are closer to each other than either is to Eukarya; but the genetics of rRNA revealed that Archaea are closer to Eukarya than they are to Bacteria. As our knowledge of the cell physiology of Archaea has increased this finding has been widely supported.

Your understanding is wrong.These dates are established by directly comparing DNA sequences.

The sequence of nucleotides

That's not the kind of information we're discussing anyway - molecular clocks, and phylogenetic trees do not care what the gene means, only what the sequence of nucleotides are. This is why they're powerful.

I think it's silly to say that a gene does not contain the information for coding a protein. Equally it's silly to think that kind of information is quantifiable.The only reason I can see for denying that the section of DNA that codes for a protein contains the information for that protein is the nonsense and equivocation we've had to put up with from Creo's regarding the information issue. I think it is a very sad day for science when we retreat for using perfectly sensible terminology for that reason.