Talk:Vertebrate visual opsin

new Vertebrate visual opsin article

Hi Martin, I noticed your focus on visual pigments and wanted to open up to your opinion. I've seen a lack of appropriate article to put a lot of information on the vertebrate visual opsins. Anything said about them in the opsin article gets buried in a sea of other much-less-researched classes of opsins and at the same time, it seems inappropriate to go into depth on only the one class of opsins in that page. On the other hand, the photopsin and rhodopsin articles (as you pointed out recently) can't handle well the distinction between apo- and holo-proteins and definitely not the discussion of porphyropsin, which for some reason redirects to photopsin at the moment...

Anyway, I wrote an article on the Vertebrate visual opsin to try and remedy this and would appreciate your input. I've put it in the mainspace, but haven't started integrating yet. Danke für Ihre Aufmerksamkeit. Curran919 (talk) 20:51, 17 November 2022 (UTC)

Hi Curran919, I agree the opsin article gets crowded with adding too much stuff about the vertebrate visual opsins. I thought about a cone opsin article, but cone opsins are a paraphyletic group, so that doesn't really make sense. So I think this is the best way do group them.

The terms photopsin and iodopsin aren't good for articles, either. Photopsin is just a synonym for apo-iodopsin and unless there isn't much more to say about it, it does not need an article of its own. The other problem with this is that it is unclear to me how it is used in the scientific literature. As far as I can see iodopsin is a synonym for LWS-opsin, in fact it is the older one and thus should be preferred. However that is just my opinion. It might also only refer to chicken red (opsin) and to those of other birds. As Shichida and his lab did. Actually, they called the chicken apo-cone-opsins R-, G-, B-photopsins, which makes things, well complicated.

So phylogenetically, you can call human red and green opsins iodopsins, but not human blue. As far as I can see calling human blue a iodopsin is a text-book invention.

About names: Today, opsin refers to the class of proteins. That is just the evolution of meaning and also because we know so much more about opsins than George Wald. I don't think that the terms iodopsin, scotopsin, cyanopsin need articles, unless you can dig up a lot of information I am not aware of. For porphyropsin there seems to be enough information available so that it can be expanded into its own article. Here is a review that should give a good start, just in case you wanna draft that article: https://doi.org/10.1016/j.ydbio.2021.03.002.

The gene encoding rhodopsin is called rhodopsin: https://www.ncbi.nlm.nih.gov/gene?cmd=retrieve&dopt=default&rn=1&list_uids=6010. Obviously, genes do not bind retinal and so it only encodes apo-rhodopsin, and since the gene is called rhodopsin it should be apo-rhodopsin, too. However, only use apo- and holo-rhodopsin if this is not clear from context, because most of the time that is clear. If we talk about sequences and relationships then it is apo. If it is about function including absorption spectra then it is holo. -- Martin Gühmann (talk) 07:02, 18 November 2022 (UTC)

Thanks for the input. This all makes sense to me, though I think some of the organic growth of early terminology like iodopsin just adds to confusion and should probably be mostly ignored unless it is critical to understanding modern literature (e.g. the rhodopsin distinction). After reading your comment, I think you are right that Photopsin should be merged into vertebrate visual opsin. I think I will do this soon. Do you think it is worth notifying Wikiproject molecular biology or just boldly merging? Curran919 (talk) 15:45, 24 November 2022 (UTC)

The other thing that adds up to the confusion is that I think that you can find this "information" in text books. From school I remember the terms rhodopsin and iodopsin. Iodopsin was the opsin of the cones. And from that it is not to far to make up three types of iodopsins, even so you don't find this in scientific research articles or reviews. At least not in articles that are close to the research. You may find it in articles that are quite far away from actual opsin research. After all this is text book knowledge, right? So you don't have to cite as everybody knows it.

However, I think it is relevant to include, as these things are floating around and it is some kind of common "knowledge". And if you want to understand the early literature that it is useful to know these terms of course in the way the are used there. Of course, you can also figure out the meaning of the early terms from the early literature, yourself. But of course, it helps to have a summary here. And it is a part of the history of the field. However, that might be a pain in the ass to figure out these things and it may be even original research doing so. For rhodopsin and scotopsin, that is still quite easy and it is enough what I put into the rhodopsin article about it. However, for the iodopsin, photopsin, and the cone opsins, it is really hard to clean up this mess, because of the text book fiction. Maybe it would be a start to just go with Wald's stuff about it and also with Shichida's and ignore the text books and the fiction, as it is hard to verify where that comes from.

For merging-in the photopsin article, you can just go ahead. At least we discussed it and we agree about it. Maybe you could just move this discussion to Talk:Vertebrate visual opsin, before you merge. So that you can show that this was not just your idea. That means if you merge you are not that bold. :D -- Martin Gühmann (talk) 05:43, 25 November 2022 (UTC)