User talk:Onco p53/Archive1

ARCHIVE ONE

Welcome

Hello Onco p53/Archive1 and welcome to Wikipedia! Hope you like it here, and stick around.

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Reminders for me

Taxobox all Actinobacteria
http://www.genoscope.cns.fr/externe/English/Projets/Projet_HF/organisme_HF.html
add genome size info? from http://www.ncbi.nlm.nih.gov/Genomes/index.html
Taxbox New Zealand Trees

Kiwi

Welcome from another Kiwi Wikipedian (from the deep south of Dunedin). Another thing that Meelar didn't say is that Wikipedians are a friendly bunch, so if you have any problems, they're only too willing to help (don't expect much from me, though, I've only been here a month or so myself!). The help pages are very useful, too, and you can always ask about any problems you have at the Village pump. Hope you enjoy it here Grutness 10:56, 11 Nov 2004 (UTC)

Fabaceae

Thanks for checking on this - when I checked the other contributions by the IP number who had changed from NO₃^- to NH₃^- (sic!), they were vandalisms, so I assumed this one was too. Should the NH₃ be changed to NH₄⁺? - MPF 10:37, 20 Dec 2004 (UTC)

This is a tricky one. You were right, that User:24.224.223.107 made a mistake (or vandalism) because they changed it to NH₃^- which is an impossible formula. The actual product of Biological Nitrogen Fixation is ammonia (NH₃), but this is immediately ionised to NH₄⁺ in an aqueous environment. The formula of BNF is:

  N₂ + 8H⁺ + 8e^-  + 16 ATP = 2NH₃  + H₂ + 16ADP + 16 Pi

NO₃^- arises by microbial oxidation of NH₄⁺. I have just had a look and none of this information is available on nitrogen fixation where I guess it should be. Should the NH₃ be changed to NH₄⁺? - well I guess so if we are looking at it from the plant perspective. It never actually uses NH₃, it has been converted to NH₄⁺ by then. Onco p53 23:08, 20 Dec 2004 (UTC)

Thanks; you know more on this one that I do, so put whatever you think best. Well worth expanding at the nitrogen fixation page, too - MPF 00:53, 21 Dec 2004 (UTC)

Will do. Onco p53 01:21, 21 Dec 2004 (UTC)

Taxobox issues

Onco, since you're about to create a tonne of proteobacteria pages, I thought I should warn you: if you leave a space between the taxobox and the start of the article's text, it gets shifted down in the final page. This is a glitch with wikitables, and hopefully it will be fixed, but in the meantime it's probably better not to leave a space. Also, note on family pages the order is not bolded and is linked, except when it is no larger than the family in question (in which case the order page is a redirect). Thanks, Josh

Cheers, nice to have some rules to go by. Onco p53 02:47, 30 Dec 2004 (UTC)

Although I always seem to get it a bit wrong Onco p53 22:44, 21 Jan 2005 (UTC)

Biochem stub

I didn't think you'd be back so soon. Visit User:Jag123/Sandbox for a list. I've excluded a few things, like a longer a-helix (which looked like a red line once shrunk) and the myoglobin I made because they looked like crap. IMO, the lipid layer doesn't look recognisable... --jag123 08:09, 1 Jan 2005 (UTC)

Errrr its the ads of the TV movie. See what the people here Wikipedia_talk:WikiProject_Stub_sorting think about them.

Yeah, I've been there. I don't really care what pic goes in there. I just want the stub. If someone doesn't like the pic or has a better one, they can go ahead and change it. This is usually simpler than asking for opinions, because you know, everyone has one of those and it's a miracle if more than two people agree ;) --jag123 15:34, 1 Jan 2005 (UTC)

I see your point, after reading the discussion on your talk page. Onco p53 23:26, 2 Jan 2005 (UTC)

Firmicutes

Hi again, Onco. Thanks for your work on Proteobacteria. Also, I notice you've started on the Firmicutes, which are a little trickier because their current classification isn't phylogenetic. Of the three classes, only Mollicutes is monophyletic, at least according to the few papers I found. I haven't been able to find details about smaller groups, or even what distinguishes Bacilli and Clostridia. I was wondering if you knew anything about them, since you'd have access to much better information than I do, working with bacteria and all that.

Thanks greatly, Josh

Hi, yep it can be tricky, especially since lots are not yet formally named (in Candidatus) so they are not really covered by the bacteriological code. Check out Phytoplasma though; see what I have done on that. Some of my colleagues are working on this, so I thought I would expand it a bit. The NCBI is OK but won't list anything that hasn't be sequenced. The IJSEM is the best journal for this. Onco p53 05:34, 18 Jan 2005 (UTC)

Also check out Taxa covered by the ICSP Subcommittee on the Taxonomy of Mollicutes Onco p53 05:56, 18 Jan 2005 (UTC)

Linking to category

I note on your user page you say you can't link to a category without the page appearing in that category. There is a way: just put a colon in front of the category, like this [[:Category:Nitrogen metabolism]] which appears as Category:Nitrogen metabolism. The same trick works if you want to link to an image without actually displaying it.-gadfium 00:42, 20 Jan 2005 (UTC)

Thanks for that, I have yet to learn all the wikipedia tricks. Onco p53 00:50, 20 Jan 2005 (UTC)

Alga

It looks like taxonomy boxes for the plants are pretty weak, I was going to have a go with Green alga any advice?. I have started something in my sandbox Onco p53 03:05, 22 Jan 2005 (UTC)

It looks ok for the most part. I would make two comments:

The kingdom should be Plantae. It's more common, and is certainly the standard that's been used here. Viridiplantae is more specific, and makes it clear what particular clade is being dicussed, but we don't necessarily want that because the division of eukaryotes into kingdoms is still variable. It looks like Plantae may end up referring to the clade with primary chloroplasts, if it is indeed genuine, and that makes a perfectly good kingdom by itself.

The green algae aren't the Chlorophyta, they also include the Charophyta and perhaps Gamophyta. Since they aren't really a taxon, I'm not sure if they should get a taxobox. They could be listed as kingdom Plantae in part, or there could be a separate page for the Chlorophyta properly, describing what separates them from the other green algae.

By the way, I don't know if you've found the full standards for the taxoboxes but in case you haven't, they're available on wikipedia:WikiProject Tree of Life. It might help you deal with some odd cases, and if you think they ought to be changed, that would be the place to bring it up.

Good luck! Josh

Check out the NBCI page. I agree on the Plantae issue, no way would I want to change all those names for questionable value.

The Gamophyta and Chlorophyta, might now be known as Zygnemophyceae. I'll try to find an actual journal review article or something. Oh and thanks for the taxbox info. I already made some changes before you replied. Onco p53 03:58, 22 Jan 2005 (UTC)

Title: Charophyte algae and land plant origins

Author(s): McCourt RM, Delwiche CF, Karol KG

Source: TRENDS IN ECOLOGY & EVOLUTION 19 (12): 661-666 DEC 2004

Document Type: Review

Have to go now, but maybe there is something in the above very recent reivew? Onco p53 04:03, 22 Jan 2005 (UTC)

Candiatus

I just found {{Taxobox section binomial candidatus}} is it possible to have something similar but for a whole genus e.g. Phytoplasma? Onco p53 10:37, 3 Feb 2005 (UTC)

I added the binomial candidatus template because the others enforce italics. You could add something similar for genera, but it isn't really necessary in the taxobox, since it doesn't affect the font. Unfortunately templates can't be chained right now. I would just use the current system, and say Candidatus Phytoplasma instead of Phytoplasma. Josh

Wikiportal biology

I thought you might be interested in this. The idea of Wikiportals was first introduced in German Wikipedia, and then it spread to French, Dutch, Polish, Hebrew and Japanese ones. This is the first one on English Wikipedia, translated from the Polish, and it's looking for people to maintain it.-gadfium 06:12, 6 Feb 2005 (UTC)

Thanks, I'll give it a go. Onco p53 04:47, 8 Feb 2005 (UTC)

Maori scientists?

Hello, Bevan, and a belated welcome if I haven't greeted you before!
Good to have another keen NZ scientist on board. If by chance any of your friends and/or associates have any contact with the Maori language, I would request that you point them in the direction of Wikipedia Maori, which has a bit of botany and a bigger bit of chemistry but could do with lots more!
Kia ora. Robin Patterson 00:06, 14 Feb 2005 (UTC)

Thank you!

Just a quick "thank you" for voting me for admin. Now all I've got to do is find out how to use these worrying new powers... Oh, and thank you for changing a couple of the NZ articles I created when I first joined Wikipedia (eg Tokomairiro River) to NZ-geo-stub, too! :) Grutness|^hello? 05:50, 15 Feb 2005 (UTC)

Stub sorting guidelines

I sincerely believe that we really need to lay down the law in stub sorting, and really provide a guideline. I believe that we should all attempt to reach a general consensus by April 2, 2005 in a set of rules that we can follow. Once we have built a set of guidelines, we can formally create a policy out of those guidelines. We need to define what a specialized topic stub is, how many articles it should cover, when is it appropriate to create it, what defines its need for its creation, what defines its need for deletion, what criteria it should follow, what are the general steps should one take when sorting a stub, whether or not to start using subst: for all templates, whether or not use subst: for all templates created by the meta-templates, and any other matters that may come up in consideration. I thank jag123 for initially creating the subpage for the project at Wikipedia_talk:WikiProject Stub sorting/Guidelines. Even though they have been discussed, I feel that we really need to confirm everything. For that, we should discuss each issue with its own sections, and raise a list of issues that we need to nail down before really continuing on. The English Wikipedia is nearly at 500k articles. Either the MediaWiki software needs to handle stubs such that they can be found with a simple union of categories, or the sorting is done manually by Wikipedians. Personally, I think the latter is less taxing on the server load, especially when we use subst:, which I think would help the Wikipedia out, performance wise. Please make your comments at Wikipedia_talk:WikiProject Stub sorting/Guidelines. I apologize for making this somewhat of a spam notice, but since the project has more members, the project can finally decide on these important issues at hand. -- AllyUnion (talk) 23:24, 15 Feb 2005 (UTC)

Cell-bio stub

No, I would not add a cell type to cell biology. I would put it in anatomy, since histology and/or cytology is a specialisation of anatomy. --jag123 12:54, 27 Feb 2005 (UTC)

BioBlitz

Hi, I was just talking to Stephanie, and that gave me the idea for a BioBlitz article. We could take a few photos in the domain, a bit of history, and overseas Blitz's too. The only problem I see is the results which would be original research. Anyway I am full on this month, and would only be able to add bits at a time, so I thought I would ask if you wanted to help out. Onco p53 02:49, 1 Mar 2005 (UTC)

Yes, I was thinking I'd do an article on BioBlitz before 12 March. I'll try to put something together this weekend.-gadfium 03:28, 1 Mar 2005 (UTC)

Kowhai in the UK

Apologies for using a Welsh photo for such an iconic NZ plant but my photos from Nelson, Dunedin and Milton were all too scrappy! I suspect that there may be many established country house gardens in the UK with Kowhai. The realisation of the botanical wealth of NZ coincided with the great growth in the British country garden tradition especially around those land-owners wanting to show off their new wealth. I know of examples at Penrhyn Castle (the photo), Bodnant Gardens and I believe at Plas Newydd on Anglesey, all within 20 miles of my home. My guess is that they are probebly reasonably common in the UK. However some NZ plants seem to prefer the milder damp climate of the west of the country and it may be that they are unusualy concentrated in Wales. It would be interesting to know whether they shared the same rhizobial communities as they do in Aukland.
Velela 07:58, 1 Apr 2005 (UTC)

Just seen this - to add that Velela's guess about an unusual concentration on the North Wales coast is correct; in Britain as a whole they are generally very rare (due to winter cold), and are only to be found planted in a handful of specialist gardens along the Atlantic coastal fringe - MPF 11:24, 15 Apr 2005 (UTC)

sections for bad stub articles

Hi,actually I am working on breaking it into sections right now. In about 10 minutes I should have brand new pages that will be much easier to work with. Thanks for helping out! Triddle 05:18, 2 May 2005 (UTC)[reply]

Excellent!, great minds and all that. Onco p53 05:21, 2 May 2005 (UTC)[reply]

ok you are ready; what do you think? Triddle 05:29, 2 May 2005 (UTC)[reply]

Well done, I was also going to suggest some instructions, which you have also done. Maybe mention the update here?. Encourage people to put Not a stub; see [[User:Triddle/stubsensor|stubsensor]] in their edit summary too, after all thats how I found out about it! Onco p53 05:44, 2 May 2005 (UTC)[reply]

Minor mistake, you spelt "edit summaries" wrong in your last change, otherwise it looks good. Onco p53 06:33, 2 May 2005 (UTC)[reply]

Hey thanks for your help with fixing those stub articles; I hope I made that page easy to use. Take it easy. Triddle 22:16, 2 May 2005 (UTC)[reply]

Advice

Hi. If you have a moment, I hope I might make use of your expertise. I'm working on another stubby article for an edible seaweed User:Pekinensis#Sea vegetable articles to create, but the thing doesn't seem to have a common name in English, so I'm planning on using the Latin one. I have a reference [1] that uses the name Meristotheca papulosa, and refers to synonyms Eucheuma papulosa and Meristotheca japonica. I could just choose the first one, but I thought I'd ask you: how would you go about deciding on an authorative name?

I have a similar question about the higher levels, which I got from another source [2].

On the other hand, both of us should really be working on our theses instead of working on this, so if you don't have time, I understand.

Thanks — Pekinensis 22:57, 10 May 2005 (UTC)[reply]

Hi, It's pretty tricky. With bacteria it’s fairly simple, there are lists of approved names, and no common names to worry about. Looking at the plants Wikiproject (which may cover algae?) they prefer common names as article titles. What we need is an authoritive source for algae taxonomy, it seems there is no formal body but algaeBASE seems good and up-to-date. I would stay away from the NCBI, as anyone can submit any name they like. The algaeBASE page for this species is: [3]. I guess you should just run with Meristotheca papulosa. One of the references was the "Marine Plants of Australia" book, but I can’t find that in my library here, these may be an English name in that. But the fact that a common name is hard to find means that is isn't well used, if one even exists.

With regards to higher-level taxa, you don't want to go there. There are disagreements amounts the taxonomists themselves about this, and it is a larger question of what Wikipedia should do. Do we follow the latest taxonomy, or stick with an older one?

Go with the taxonomy you have on your page, we can always fix it later if there is a consensus. Onco p53 00:11, 11 May 2005 (UTC)[reply]

Thank you! That was very helpful and informative. I will follow your suggestions. — Pekinensis 01:49, 11 May 2005 (UTC)[reply]

One more thing, excellent changes on Sea lettuce, I am used to writing for scientists. One point though, don't leave a gap after {Taxobox_end} and the beginning of the article, it for some reason creates extra space at the top of the page. Onco p53 21:37, 11 May 2005 (UTC)[reply]

Meristotheca and Meristotheca papulosa are in place. The former is very short, and the latter is very rough. The lower sections are a direct translation of my first reference above, and demonstrate my limited translation abilities and dim hobbyist's understanding of biological terminology. I have commented out several sentences (and bolded the particular words) of which I was most unsure, with the thought that you (or a future editor) might review them.

— Pekinensis 01:36, 13 May 2005 (UTC)[reply]