Comments by "Angry Kittens" (@AngryKittens) on "Are We All Actually Archaea?" video.

@shawnwales696 Phylogenetics is about genetic relationships. Not mere distinguishing "criteria". You're comparing a far larger amount of genes, and are thus more accurate, not just a short list of characteristics. It's like the difference between determining the father of a child by genetic paternity testing, vs. seeing if the child has blue eyes and red hair, etc. As weird as it may sound, there are quite a few (anaerobic) eukaryotes that have secondarily lost mitochondira completely, only retain vestigial mitochondrial organelles (like mitosomes), or have formed symbioses with completely different bacteria altogether.
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@EebstertheGreat We can, but it's not as straightforward as organisms since they can not self-replicate. VIruses are more like independent proteins, like prions. They are believed to have arisen multiple times from various different sources, from at least several viable means. There is no single lineage of viruses. Phylogenies for specific viral clades with common ancestors is possible, and look pretty much like what the tree of life does. But integrating them into the wider phylogeny of living organisms is problematic, since unlike living organisms, they don't stay within the branches they arose from. They literally replicate by merging into other branches of life. In a lot of cases, those merges become permanent. Humans, for example, contain quite a large amount of viral genes (8% of our total genome!) that have become literally part of our DNA (human endogenous retroviruses - HERVs), most inactive, but some are believed to reactivate in some conditions and be the cause of autoimmune disorders and cancers. They can be separately classified into three clades based on genetic similarities. But in terms of the wider tree of life, they would technically be in the human branch, because they are in humans.
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@EebstertheGreat But how do you do that? Viruses are gene robbers with a very high rate of HGT (almost always cell -> virus), far higher than bacteria and archaeans. They are extremely genetically diverse, far more than living organisms, precisely because of that. The viruses we've found to have seemingly vestigial metabolic/translation genes that imply a regressed organismal "ancestor" turned out to have instead stolen those genes from their hosts. Any trace of what their "original" genome looks like would be either far gone, or completely unrecognizable by now. Whether they arose before the first cells, or from cells, or both, is unknowable.
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@Gelatinocyte2 Nowhere did I say viruses were proteins. I said they are LIKE prions, in that they can not self-replicate, in response to someone asking if we could classify viruses like living organisms.
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@Gelatinocyte2 What are you even talking about. 1. Neither of them SELF-replicate. In the proper sense of the term. 2. Both of them REPLICATE. Prions by inducing healthy preexisting proteins to misfold. Viruses (and viroids) by hijacking cellular reproductive machinery. 3. Neither of them use "raw materials" from a host cell. They do not eat/break down the host cell for components. Viruses "become" the cell by inserting itself. Prions "convert" preexisting proteins. 4. None of them can be easily classified phylogenetically, in the same way living organisms can. Viruses are classified by morphology, while prions are not classified at all. THAT is the point of this discussion, as started by the original commenter who asked where viruses are in the tree of life.
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@Gelatinocyte2 You seem to be deliberately conflating self-replication (having the mechanisms for making copies), with DNA replication (copying DNA specifically), with replication in general (creating more copies). Prions make more prions, that is replication. It's not GENETIC replication, but it's still replication, and the entire reason why it's infectious and not just a normal protein. A cell's reproductive machinery is NOT "raw material", it's the factory. Even if you put a virus into a soup of all the nucleotides it is composed of, it will just sit there doing nothing without all the necessary mechanisms of a LIVING cell capable of accepting the virus's blueprint. I KNOW there have been attempts to phylogenetically classify viruses. I clearly said that in my original comment. I also clearly explained why it's still difficult to trace their lineages in the tree of life. Not a separate "tree of viruses" (which given how viruses may have multiple origins, is impossible), but the COMMON tree of LIFE, that all living organisms share. Just because viruses are genetic, doesn't mean we can classify them phylogenetically as easily as living organisms. Viruses (and viroids) mutate extremely quickly, and due to their mode of replication, they can break and carry off genes from hosts and vice versa (a very important evolutionary mechanism in microbial evolution), muddying the water by implying connections that aren't actually by descent. They STEAL genes. For this reason, the International Committee on Taxonomy of Viruses classify viruses by their FORMS. Not their genes. Unlike other governing taxonomic bodies which in modern times, are phylogenetic. You're jumping in the middle of the conversation swinging wildly.
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@Gelatinocyte2 If you expect me to continue arguing about the semantics of replication (or "proliferation", as the synonym of choice you've chosen, also try "propagation" 🙄), you're sadly mistaken. I've already explained it above. Maybe go yell at the authors who named it the "Prion replication cycle". I'm not interested.
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@Gelatinocyte2 Right. You latched unto a single sentence and ignored everything else, including the context. That was obvious. Then you latched unto terminology. From replication, now you're arguing with yourself about proliferation. Oh, and it's not a paper, or a title. That is literally the terminology everyone uses. Replication. And everyone knows precisely what that means. Including the glaring fact that viruses and prions do not replicate in the same way. You're the only here hung up on semantics in an effort to sound like you actually have something to add to the conversation. You don't. Go away.
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