Ypna

Organisms et al.

Hello. I hope you’re doing well, my friend. If you don’t mind, I’d like to ask you for advice. According to the taxoboxes, plastids are classified within the phylum Cyanobacteria (see: plastid and Cyanobacteria); additionally, the article Endosymbiont explicitly states that both the mitochondrion and plastids are considered bacterial endosymbionts. Some sources, such as the Tree of Life Web Project, tend to include these organelles in the domain Bacteria, the quotation: Eubacteria ("True bacteria", mitochondria, and chloroplasts). Can we assume that the domain (Eu)Bacteria listed in the template already covers mitochondria and plastids, or should they be put in there in any way, shape, or form? Thank you in advance. Greetings, --Jojnee (talk) 18:30, 23 January 2021 (UTC)

Hello my friend! The facts only say that plastids are somewhat different to non-plasid bacteria, but biologists ultimately need to make an arbitrary decision: (1) classify plastids as genuine but unusual bacteria, giving species Latin names, assigning them to genera, etc., or (2) consider plastids as a category of unusual organelles with some bacteria-like properties since they are of bacterial origin. To my understanding, no. 2 is the conventional interpretation, probably for the sake of convenience. Other wise there'd be an Alphaproteobacteria (mitochondrial) species for all eukaryotes plus a Cyanobacteria (chloroplast) species for photosynthetic eukaryotes. In summary, I think "bacteria" is normally interpreted to exclude plastids, so I think we're justified in listing plastids separately. Ypna (talk) 07:52, 24 January 2021 (UTC)

Thank you very much. Yes, I totally agree with you. Although the researchers stated that the phylum Cyanobacteria includes free-living bacteria and plastids (see: here), and discussed the phylogenetic placement of mitochondria within the Alphaproteobacteria (see: here), plastids and mitochondria themselves are still defined as organelles but not independent organisms. Therefore, I propose to add the mitochondrion and plastids to the template. However, I must admit that I don’t know where exactly, hence I would appreciate your help. By the way, I was also wondering about the last universal common ancestor, but (de facto) it appears to be already covered by the Earliest known life forms, especially since the LUCA is mentioned and described in a section of this article, don’t you think? Warm regards, --Jojnee (talk) 14:30, 24 January 2021 (UTC)

It's certainly possible to research which cyanobacteria are most closely related to plastids and so on, but at the end of the day the bacterial taxonomists don't actually classify any plastid as a formal species. Anyway, I assumed plastids and mitochondria were already included in the navbox by now. I found a place to insert plastid and mitochondria; have a look and tell me what you think. Regarding LUCA, I'm not convinced this needs to be included since it's not really a distinct kind of organism or organism-like thing, rather, it's a concept (probably?) corresponding to some ancient bacterial/prokaryotic species. Ypna (talk) 00:19, 25 January 2021 (UTC)

Thank you very much. I think that mitochondria and plastids fit perfectly there. Re. the LUCA, yes exactly, plus it is (de facto) included within the category Earliest life forms. It’s always a pleasure cooperating with you. Have a nice a day! --Jojnee (talk) 09:30, 25 January 2021 (UTC)

After doing some research, I thought that perhaps it might be reasonable to add the LUCA to the template. For more information, please check the following paper: the link. I found it to be very interesting, the quotation: Three different views of LUCA could be easily imagined: (1) LUCA was a prokaryote (i.e., bacterium or archeon), (2) LUCA was rather eukaryotic-like than prokaryotic-like; (3) LUCA was neither prokaryotic- nor eukaryotic-like. However, since the LUCA is not a distinct category of organisms, I suggest including it in brackets within the Earliest life forms. I hope you will accept my proposal. Either way, thanks a lot for your help, I greatly appreciate it. --Jojnee (talk) 18:44, 27 January 2021 (UTC)

Ok, sure thing. I added it exactly where you proposed. Also note that I don't 'own' the template so you're welcome to be bold and make changes if you feel confident. Cheers. Ypna (talk) 13:17, 28 January 2021 (UTC)

Thank you very much. Yes, I know. However, I have to admit that I highly value your opinion; thus, I firstly prefer to discuss with you any matter regarding potential additions to the template. And besides, I take this as a great opportunity to exchange a few words and cooperate with you, which I always enjoy :) I hope that you don't mind it. PS. I added the navbox to the articles Mitochondrion, Plastid and LUCA. Cheers, --Jojnee (talk) 16:00, 31 January 2021 (UTC)

I'm flattered to hear you think so highly of my opinion! It's a pleasure to cooperate with you. And thanks for adding those links; I should have done that but I forgot. Ypna (talk) 21:52, 31 January 2021 (UTC)

Hi. Thank you for the recent edit. Now, the virus section looks much better. However, I would suggest to keep the links to various subviral agents (viroids, satellites), especially since it's not easy to weave them within viral taxa, and some of them (e.g., virusoids) aren’t assigned formal taxa at all. I hope you’ll accept my proposal. Regards, --Jojnee (talk) 23:45, 3 February 2021 (UTC)

Thanks for the feedback, I appreciate that. I've restored the subviral agent links. Cheers. Ypna (talk) 03:04, 4 February 2021 (UTC)

Hi. Recently, a new article whose subject seems to fall within the scope of the template has been created. I mean the article Bio-like structure. The only concern might be that these entities are most likely inorganic structures; however, they were reported to exhibit enzyme activity. Moreover, a cursory review of the scientific literature on the matter leads to the conclusion that the structures obtained by V. O. Kalinenko are discussed in a similar context as coacervates, proteinoids and "Jeewanu"; on a side note, the concept itself slightly resembles that of jeewanu. This is a somewhat borderline case, but I believe that the presented arguments should be sufficient (especially since we are not talking about, let's say, robots, etc.). Therefore, I suggest adding bio-like structures to the navbox (and, vice versa, the navbox to the article). What are you thoughts? I hope you'll accept my proposal. PS. The topic in question is quite interesting. Warm regards, --Jojnee (talk) 00:00, 15 February 2021 (UTC)

Yes, that article seems to belong in the bottom section of the navbox. I added the navbox to that article, and the article to the navbox; this has forced me to removed the word "organic" from "comparable organic structures" since bio-like structures are inorganic. I also decided to alphabetise the links in the navbox. Ypna (talk) 00:54, 15 February 2021 (UTC)

As always, you've done it in the best possible way. Now, it really looks great. Thank you. I think there is one more kind of organic structure that surely belongs in the scope of the template. I mean the so-called Spiegelman's monster, a bacteriophage Qβ-derived non-coding RNA molecule capable of self-replication under artificial conditions. This proposal seems to be rather uncontroversial, I believe. However, I don't know where exactly it should be included. I'd like to rely on your intuition once again, especially since you are an expert on virus-related topics. PS. The article in question can be found here. --Jojnee (talk) 22:00, 15 February 2021 (UTC)

Oh Spiegelman's Monster. Yeah, it belongs in the navbox. I just placed it in the the Comparable structures section since it is neither 'life' in the traditional sense nor a virus. "Expert" is a little bit of a stretch at this stage but I'm hoping to grow into that title. Ypna (talk) 23:18, 15 February 2021 (UTC)

Thank you very much. I'm certain you'll achieve your goal, my friend! Best wishes, --Jojnee (talk) 07:00, 16 February 2021 (UTC)

Hi. I hope you are staying healthy and safe during these uneasy times. Recently, one more article whose subject seems to fall within the scope of the template has been created. I mean the article Integrative and conjugative element. ICEs appear to resemble both plasmids and transposable elements. Therefore, I suggest adding ICEs to the navbox (and, vice versa, the navbox to the article). What are you thoughts? Cheers, --Jojnee (talk) 00:00, 5 March 2021 (UTC)

Hello Jojnee. Yes I am in good health, thank you. Thanks also for keeping track of these emerging articles. Your suggestion seems appropriate; I included the article into the navbox, and vice versa. Regards, Ypna (talk) 04:31, 5 March 2021 (UTC)

Hi again, my friend. Recently, while reading some papers, I realised that the template lacks one (quite important) category of organism-comparable structures. Specifically, Eugene V. Koonin and Valerian V. Dolja, in their concept of the "greater" virus world, discuss retroelements that constitute a diverse category of virus-like agents; please check the following links: A virocentric perspective on the evolution of life, Virus World as an Evolutionary Network of Viruses and Capsidless Selfish Elements. Many retroelements are already included in the template, as LTR, non-LTR and Penelope-like retrotransposons are transposable elements (Class I TEs), the so-called retroplasmids are plasmids present in the mitochondria of some fungi and group II introns are ribozymes; still, there is a variety of retroelements that do not fall into any of these categories. Since the entry "Retroelement" redirects to the article Retrotransposon, but dedicated articles (rightly) use the term "retroelements" to describe other genetic elements, e.g. retrons, I suggest adding the category Other retroelements (or perhaps unclassified?) to the navbox, and subsequently put in brackets the remaining elements, as follows: retrons, diversity-generating retroelements (DGR), telomerase reverse transcriptase (TERT) and RT-related cellular genes (rvt). I must admit that I have doubts regarding the technical details (other/unclassified?, full names of retroelements versus acronyms, etc.), so I decided to contact you and rely on your unerring intuition. I hope you will accept my proposal, especially since it seems to be rather uncontroversial. Thanks a lot! Regards, --Jojnee (talk) 15:59, 14 July 2021 (UTC)

Hello my friend, Jojnee. I see you're still expanding your mind with interesting literature. While I've read neither article before, the core message of the second paper (repeated transitions between encapsidated and capsidless selfish genetic elements) was fairly familiar to me so I skimmed through it. When I learnt of this several years ago, I began thinking of and using the word 'virus' in a broader sense comparable to their 'greater virus world', including things like viroids, satellites, and some transposons). I read the first paper entirely and I enjoyed thinking about viruses as sort of genetic playground where the full suite of replication strategies are explored, and retro- and RNA-viruses as perhaps the principal source of genetic variation on earth, through mutation followed by horizontal gene transfer. Thanks for sharing these with me.

Now to the navbox. I agree with your proposal. But your description of my inuition as "unerring" is too kind and far from true; you might be over-estimating my knowledge as I'm also unsure about the technical details of implementing your suggestion. So, since you seem to have thought about this more than I have, I propose you take the liberty to have a go at it, and I'll check the navbox afterwards and see if I can make any tweaks or if further changes are needed. Regards, Ypna (talk) 01:45, 15 July 2021 (UTC)

P.S. You might also like to review at an attempt of mine to summarise the relationships between viruses and virus-like entities, here. Ypna (talk) 02:28, 15 July 2021 (UTC)

Thank you for the reply. After some thoughts, I believe we should choose between the following options: either (a) Retroelements not elsewhere classified (Retron, DGR, TERT, rvt), or (b) (other?) Retroelement (Retron, Diversity-generating retroelement, Telomerase reverse transcriptase, Reverse transcriptase-related cellular gene). Alternatively, we could omit rvts as currently no article regarding them exists (it definitely should be created, though); additionally, there are other (less important) classes, e.g. RT-like mitochondrial ORFs of Chlamydomonas, but they probably don't deserve to have separate articles, so we can just assume them to be (de facto) included by generally falling under this category. On a side note, it seems reasonable to distinguish the terms Retrotransposon and Retroelement, especially since the latter covers a (much) wider spectrum of genetic elements, but that's another story. Thanks a lot for the link, it's a very interesting topic! PS. Your intuition has proven truly reliable, and I highly value it. Kind regards, --Jojnee (talk) 09:59, 15 July 2021 (UTC)

Ok, well option (a) looks slightly more refined to me. Yes, Reverse transcriptase-related cellular gene can go in the navbox as it shouldn't remain red for long. I may do some work on it. Ypna (talk) 02:34, 16 July 2021 (UTC)

I made Reverse transcriptase-related cellular gene a redirect to the 'In cellular life' section of Reverse transcriptase, for now. Ypna (talk) 23:16, 18 July 2021 (UTC)

Thank you very much. I can always count on you, my friend. Until an article on RVTs is created, the temporary redirect seems a reasonable idea. Yes, I agree with you, I think that the first option would be a better choice. If no further adjustments are required, it can be added to the navbox, I believe. PS. I apologise for the late reply. Recently, I've been very busy in real life. Warm regards, --Jojnee (talk) 22:30, 19 July 2021 (UTC)

 Done Please review the edit, and feel free to make further changes if any tweaks are needed. Also, I've added the navbox where it was missing; however, I skipped Reverse transcriptase-related cellular gene, since it's a redirect page. PS. I corrected a wikilink to the article Retroposon. Regards, --Jojnee (talk) 13:15, 27 July 2021 (UTC)

Thanks for making these additions. I like it as it is and have no modifications to make. I do have two new ideas: shall we add mobile genetic element somewhere? And shall we move the name of the navbox to reflect the current title (Organisms et al. ––> Life, non-cellular life, and comparable structures)? Regards, Ypna (talk) 23:23, 27 July 2021 (UTC)

Thank you very much, my friend. Regarding mobile genetic elements, the main problem is the term seems vague, i.e. it lacks a precise definition. Considering that various MGEs (e.g. plasmids, transposable elements, group I and II introns being ribozymes, integrative and conjugative elements) are already included in the navbox, I would suggest, at least for now, staying with the current version. Of course, this is only my personal opinion, and thus I'll rely on your intuition here. As for renaming the template, I think it's a reasonable idea. If you find it necessary, it'll be an uncontroversial change. PS. Are you planning to create a stub article on RT-related cellular genes (RVTs)? Warm regards, --Jojnee (talk) 05:00, 28 July 2021 (UTC)

Yes, 'MGE' is vague and encompasses several links already included, making it unclear how it could be integrated into the navbox. I'll make the move now, as I think it makes sense for the navbox to have the same name as the navbox's title. Regarding RE-related cellular genes; I'm not knowledgeable in this area at all. Perhaps you could create the stub? Ypna (talk) 00:40, 29 July 2021 (UTC)

Great job! Well, this is undoubtedly a redirect with possibilities. --Jojnee (talk) 00:45, 30 July 2021 (UTC)

Hello again. I hope you are doing well, my friend. Recently, retrozymes have been added to the navbox. To be honest, I am not a big fan of this edit, but I don’t mind it either. However, the current order of subviral agents seems a bit chaotic. Virophages and virusoids are satellites, and retrozymes are (nonautonomous) retrotransposons. Or perhaps it was intentional? If you find some time, could you have a look at it, please? Cheers, Jojnee (talk) 22:00, 22 January 2022 (UTC)

Hello again. Retrozyme certainly don't belong in that list of subviral agents, and I suppose it's already covered by Transposable element. I've reverted the edit. I also agree that the subviral agents section is a bit chaotic, but I don't know if there's any way to organise them in the navbox that would satisfy the complex and varied relationships between these different categories. How about removing the list and renaming the section Viruses and subviral agents, and readers can click on the subviral agents link to see more details? Ypna (talk) 20:40, 23 January 2022 (UTC)

Yes, I agree with you. Thank you very much! Regarding subviral agents, I would keep the current list, especially since the term Subviral agents is vague and may or may not include prions. Actually, after your edit, the list seems fine. Perhaps a new ICTV taxonomy release will shed some light on the issue? Cheers, Jojnee (talk) 14:30, 24 January 2022 (UTC)

You're welcome Jojnee. With this list of subviral agents, my thinking when I wrote it was that it is just a list of terms used to refer to unusual viruses/virus-like things, with no attempt to organise them into a logical Venn-diagram or any other system. Strangely, I find myself looking forward to next ICTV release – can't wait to find out which taxa will get placed in existing or new realms. Ypna (talk) 03:27, 25 January 2022 (UTC)

Hi again Ypna, I've updated the navbox. If you have some time, could you review my edit, please? Cheers, Jojnee (talk) 20:45, 17 August 2023 (UTC)

Hi Jojnee. Yes your recent edit makes it a bit cleaner, thanks. I also just shortened a link from displaying "Satellite (biology)" to just "Satellite", but still linking to the same destination. It's clear from the context that it's the biological satellites that are being referred to. Ypna (talk) 23:18, 17 August 2023 (UTC)

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A barnstar for your efforts

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