[DoctorOetker]

> You could make an argument they are "viroid-like" and there's a deeper evolutionary connection between viroids/viruses/plasmids, but the information theory to formally establish such a connection is not sufficiently developed.

The way it is phrased, insufficiently developed information theory is rather surprising. Did you mean to write that not enough genome data has been collected to formally establish a link, or are you actually stating that we have all the data but as a species have not sufficiently developed the mathematical subdiscipline of probability, information theory ?

I could follow the first, but the latter?

EDIT: I now believe you meant neither but more something along the lines of: we probably have plenty of data, and usual information theory should suffice, but we simply havent exhaustively applied the tools to collate the information and make the implicitly available data more explicitly manifest.

[ababaian]

We certainly have the data, too much so actually. I should correct the statement to say, we have insufficiently developed _applied_ information theory.

We know how to quantify homology, it just has not been applied to sufficient depth to the field of RNA/viroid evolution to resolve how much of an RNA element with extensive secondary structure, or ribozyme is evidence of a homology vs. convergence. And how could we resolve the two? It's easy with protein sequences, tricky with protein structures, but deep RNA evolution? That's a mystery.