Let us look in detail at the catalytic properties of RNA. The single intron of the large ribosomal RNA of Tetrahymena thermophila (a ciliated protozoan) has self-splicing activity in vitro. This RNA was named a ribozyme because it is an RNA that acts like an enzyme. However, most, if not all other RNA-based catalytic reactions are thought to take place in conjunction with proteins. Spliceosome and ribosomal RNAs have the ability to catalyse peptide bond formation, but they are better described as catalytic ribonucleoproteins than ribozymes since they do not make the role of proteins unnecessary.
Large ribozymes mostly include members of the group I and group II intron family found in algae, fungi and plants. These are self-splicing introns. Group I ribozymes use an external guanosine (G) nucleotide as a cofactor and group II ribozymes require an active site containing Mg2+ ions for catalysis. Group I and group II introns self-splice under certain conditions in vitro, but require proteins to fold the intron RNA into the catalytically active structure in vivo. The proteins are either encoded by the introns themselves or encoded by other genes (Allison 2007, pages 69-73 and 455-457).
Small ribozymes found in viruses and viroids act as riboswitches involved in gene regulation. The other small ribozymes are involved in self-replication of the circular RNA of viruses (Allison 2007, page 75).
From this detailed account it can be seen that ribozymes represent a limited case found in a few organisms. Intron-splicing by a ribozyme is catalytic and leads to modification of the RNA itself. This characteristic contradicts the classic definition of an enzyme as being a substance that increases the rate of a chemical reaction, but is not itself changed in the process. Therefore, a ribozyme does not simply act as an enzyme made of RNA rather than protein.
The autocatalytic nature of RNAs cited as ribozymes is highly questionable when one pays attention to detail. It emerges that in vivo none of these RNAs act alone – their catalytic properties are dependent on proteins to initiate folding that makes the RNA structure catalytically active. Therefore, RNA ribozymes do not act alone, but in conjunction with proteins. It looks like proteins won’t go away.
I have not used the word hypothesis in connection with RNA World because it is untestable. It is a speculation upheld by an almost mystical view of Natural Selection in which Natural Selection acts in a world of personified molecules that ‘want’ to replicate. Shapiro accuses the adherents of these origin of life theories as creating a mythology whose truth cannot be challenged even in the face of adverse evidence (Shapiro, 1986, page 32).
“In the origin-of-life field, a particular theory or point of view is frequently elevated to the status of a myth. It is then treated only as a doctrine to be validated, and not one to be challenged.” (Shapiro 1986, page 33).