I think there may be a reasonable missunderstanding here. He's using the information on DNA analogy that provides an understanding of DNA. The one that states, gene's are encoded into the DNA's sequence but aren't the DNA. This can be thought of in computer terms. A digital picture of my foot on a harddrive is composed of electrons organized into a pattern, but this digital file wouldn't be considered mere electrons. That's just the medium it is written onto.
Now, I think that this reasoning (while useful for interpretations) is a false analogy. The digital foot photo is a seperate bit of information that was written onto the hardrive and is not of the harddrive. However, genes encoded on DNA/RNA can not be seperated from the molecules by which they are on. This is because genes are not exact a priori sequences that had to be hit initially. They were just the sequences that provided some advantage in what ever system they were in to begin with.
Actually, one person on this thread seems to think that a gene equals a molecule and that is not the only misunderstanding floating around here.
Technically, and the distinction does matter, DNA sequence is data not information. I consider data, not genes to be the fundamental quantity of evolution. In my view, genes format some of the data in DNA. The data in a gene becomes information when it is interpreted into some biochemical activity and, I would argue, it is the biochmical activity that is the information. The code that performs that translation must have arisen at the same time that base sequence became significant. Thus base sequence is not the only data on a genome that is biologically significant. The choice of bases and determinants of the code are also important. At a grosser level, so is the sequence of genes on a genome.
Nobody does experiments with self-replicating nucleic acids. Here I write purely from memory but the first studies to make that kind of claim came from Spiegelman's laboratory. He worked on Qbeta, a phage that produces a RNA directed RNA polymerase. So he took his polymerase, some RNA, I think from the phage, and the necessary chemical substrates then he let it run and in that test tube it evolved. As I recall, it selected smaller molecular weight RNAs but that detail is not important.
What is important is that he provided the necessary enyme and substrates, no nucleic acid can do without such hand-holding and this kind of thing is not workable as a theory for evolution. Crick tried to calculate the probability of such self-contained systems arising by chance and he surrendered, eventually proposing, as a MORE realistic alternative, that life must have come to earth in spaceships.
The other popular nonsense is enzyme hypercycles which, I vaguely recall come from Schuster on the continent. These too are highly unlikely and Orgel, another well known advocate of spaceships, described such thinking as an appeal to magic. I agree with him about the magic but not about the spaceships.
So note clearly, Kleinman is right. There are no self-replicating molecules in the cell. Not RNA, DNA or protein. I know of no sensible reason to believe that any such molecule could ever self-replicate. The smallest known self-replicating entities in biology today are cells and I do not believe that there was ever a replicator comprising one single molecule or even a small number of molecules.
Finally, Paul, I am sure there are some exceptions but nucleic acids are not generally immunogenic and are therefore unlikely to be of value as a vaccines. In the main, it is proteins and complex carbohydrates, such as the sidechains on glycoproteins and glycolipids, that generate immune responses. I therefore think your comments on vaccines must be wide of the mark.
