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The OP addresses it to some degree, but how does this fit with the fundamental classes of phylogeny? My poor understanding has been that there are cellular org

by mmooss 2y ago

The OP addresses it to some degree, but how does this fit with the fundamental classes of phylogeny? My poor understanding has been that there are cellular organisms / 'biota' (if those are the right terms - prokaryotes, eukaryotes, etc.) and viruses. Where do obelisks, Virus-Viroid Hybrids, Zeta-Elements, Ambiviruses all fit in that scheme, if they do at all? Or is there a new scheme? And it is very cool for you to answer questions here. Remember us if you visit Sweden someday! :)

ababaian 2y ago
The classic phylogenetic classes are a fantastic model, but https://en.wikipedia.org/wiki/All_models_are_wrong https://en.wikipedia.org/wiki/All_models_are_wrong :) Phylogeny is the study by which things relate to one another. There is a divergence point at which point it becomes impossible to relate two sequences to one another. Obelisks, Zeta-Elements, Deltaviruses, viroids all veer towards their own divergence point into infinity, but their are higher-order genome organization traits which are consistent. We don't know if these traits are the same by origin, or the same by chance. Interestingly Ambiviruses also have this genome organization, but they have a protein which is de facto of an RNA virus. My opinion is that these simple genome layouts (structured circular RNA elements with ribozymes) are like a cauldron of mixing simple genes, and when they come together just the right way, we see those lineages take off. Think of it as an ocean of ancient primordial RNA replicators, ready to fire off, and this process is ongoing even today.
- mmooss 2y ago
  Thank you. > The classic phylogenetic classes are a fantastic model, but https://en.wikipedia.org/wiki/All_models_are_wrong https://en.wikipedia.org/wiki/All_models_are_wrong :) For the record, yes, I know. Unfortunately, we need models to organize the world in our limited brains, and the less intimate experience one has of something, the more simplified their model. This isn't my day job! :)

by mmooss 2y ago

ababaian 2y ago

The classic phylogenetic classes are a fantastic model, but https://en.wikipedia.org/wiki/All_models_are_wrong https://en.wikipedia.org/wiki/All_models_are_wrong :) Phylogeny is the study by which things relate to one another. There is a divergence point at which point it becomes impossible to relate two sequences to one another. Obelisks, Zeta-Elements, Deltaviruses, viroids all veer towards their own divergence point into infinity, but their are higher-order genome organization traits which are consistent. We don't know if these traits are the same by origin, or the same by chance. Interestingly Ambiviruses also have this genome organization, but they have a protein which is de facto of an RNA virus. My opinion is that these simple genome layouts (structured circular RNA elements with ribozymes) are like a cauldron of mixing simple genes, and when they come together just the right way, we see those lineages take off. Think of it as an ocean of ancient primordial RNA replicators, ready to fire off, and this process is ongoing even today.

mmooss 2y ago
Thank you. > The classic phylogenetic classes are a fantastic model, but https://en.wikipedia.org/wiki/All_models_are_wrong https://en.wikipedia.org/wiki/All_models_are_wrong :) For the record, yes, I know. Unfortunately, we need models to organize the world in our limited brains, and the less intimate experience one has of something, the more simplified their model. This isn't my day job! :)