User talk:Peter coxhead
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Plant article naming convention
Hi Peter coxhead. There is a plant article naming convention request at the Help Desk. I saw your name listed at Naming_conventions_(flora) contributions and am hoping you would post your thoughts at How long does speedy deletion usually take?. I asked Pmanderson on the Pmanderson talk page, but not sure if she/he will see the request. Thanks. --
Hey thank you for editing . My friend
Hi, I'm still in the learning process of adding ethnopharmacological based information to Wikipedia. I don't disagree with your subtracting out the references to the animal based studies at all.
If I happen to run across one or more clinical studies, would I be able to run it by you beforehand, as a preemptive 'peer review'? [posted by User:Chango369w)
- Well, I'm not by any means an expert on this topic. If you haven't done so, you need to read WP:MEDRS; personally I think that the way it's interpreted by some editors is sometimes unnecessarily strong, but it is the standard to be followed. The two key points seem to me to be:
- We are always free to, and inded should, report established ethnobotanical uses for plants, whatever those uses are, including uses in traditional medicine.
- Research related to use in traditional medicine should only be reported if it meets the standards of MEDRS, i.e. there are reliable reviews. It's not appropriate to report "research in progress" or "investigations proceeding", nor to report in vitro or animal studies.
- By all means ask if you think I can help. WT:MED is where the real experts hang out!
- By the way, don't forget to sign your posts with ~~~~. Peter coxhead (talk) 08:03, 25 July 2015 (UTC)
- I'm not sure that we can include anything about ethnopharmacology on Wikipedia under MEDRS. By definition, the field is at the intersection between ethnobotany and clinical medicine. There's this quip, "what do you call alternative medicine that works?" : "Medicine". Ethnopharmacology is about (potentially) validating ethnobotanical use clinically, but it's the phase in the process where the research is mostly in vitro or in animal models. When you search Google scholar for the vast majority of plant species, the results are taxonomic and ecological studies. For a handful of plant species, the literature is dominated by ethnopharmacological studies, and it ought to be possible to mention that somehow, but it is tricky to do while complying with MEDRS. It would help if Wikipedia had an article on ethnopharmacology (there was a stub that was merged into ethnomedicine, but it's certainly a topic deserving of it's own article). Plantdrew (talk) 18:59, 25 July 2015 (UTC)
- @Plantdrew: It's tricky, I agree. Some thoughts:
- We can say that the plant has an ethnobotanical use, including traditional medicine, and what this use is.
- Under phytochemistry, we can say what compounds it contains that are known to be biologically active in animals, and what their effects are.
- If the plant is in any of the reputable pharmacopeias, we can say this and what it's listed for. There are traditional preparations in the British Pharmacopeia (I don't know about the US equivalent); the first such I found in the index was "Acanthopanax Bark". We would need to be careful not to imply efficacy unless there is WP:MEDRS-compliant evidence.
- The difficult issue is reporting that active research is going on. WP:MEDANIMAL doesn't forbid altogether reporting animal and in vitro studies. If there are many studies – ideally with a substantial review – then they can be mentioned, so long as it's made clear that they don't provide any evidence to support use in humans.
- Anything more? Peter coxhead (talk) 19:51, 25 July 2015 (UTC)
- @Plantdrew: It's tricky, I agree. Some thoughts:
Per the debate here, which is rapidly beginning to generate more heat than light, I'd be interested to know if you could point me to any third-party sources that verify that this is a valid concept. I respect your knowledge base and you seem to know the topic better than some of the other folks debating it. Montanabw(talk) 08:39, 27 July 2015 (UTC)
- I agree about the "more heat than light". The discussion seems to me to be typical of those we have in Wikipedia when dealing with ill-defined concepts that have a core meaning but whose detailed meaning varies by context. "Race" in the context of the classification of organisms does seem to me to be worth an article, which would deal with (1) the broad historical use of the term for infraspecific classification (2) the current use, limited to some groups like fungi, otherwise now largely abandoned in favour of concepts like subspecies or clines. I'll have to think more about sources! Peter coxhead (talk) 13:33, 27 July 2015 (UTC)
Cross-posted form my "talk" page
You undid an edit I made to the cladogram page, saying that "this must be discussed first." You have not seen fit to start that conversation so I will. The section I wrote is based on what is stated - apparently unobjectionably - in the earlier part of the Cladogram article:
"a cladogram is a diagram used in cladistics which shows relations among organisms. A cladogram is not, however, an evolutionary tree because it does not show how ancestors are related to descendants or how much they have changed; many evolutionary trees can be inferred from a single cladogram ..."
"Researchers must decide which character states are "ancestral" (plesiomorphies) and which are derived (synapomorphies), because only synapomorphic character states provide evidence of grouping. "
Phenetic algorithms do not use outgroups, and neither they nor ML or Bayesian methods group by synapomorphy alone.. This is why the material in the "Selecting a cladogram" section is incorrect - particularly, the statement "Algorithms for cladograms include least squares, neighbor-joining, parsimony, maximum likelihood, and Bayesian inference." These things are not "cladistics" and do not, therefore, produce "cladograms." Abrower (talk) 12:26, 31 July 2015 (UTC)
- Apologies; I thought you would understand that the comments I made are on the talk page of the article. See Talk:Cladogram#What is and is not a cladogram. Please respond there so that others interested in this topic can join in. Peter coxhead (talk) 12:33, 31 July 2015 (UTC)
Hello, Peter - I just reverted an edit to Cinnamon. While there, I again noticed the image in the lead. I think I had left a comment months ago either at User:Sminthopsis84's talk page or on the article's talk page (can't remember now) when the lead image was changed to this one. I really liked the previous image better. It showed cinnamon sticks up close. Even if that earlier one can't be found or you don't like that one, couldn't we find a better photo of cinnamon sticks than the one that is there now? In the image that is there, the cinnamon sticks are so skinny and far away that they look like pencils, and there is no need for a pile of cinnamon powder in an image labeled "cinnamon sticks". The powder can be shown later in the article. What do you think? Can you either restore the one that was there before or find another image? CorinneSD (talk) 02:54, 1 August 2015 (UTC)
- @CorinneSD: yes, I agree that the image wasn't the best. I created a lighter version of the rather dark one that used to be there; what do you think of that? Peter coxhead (talk) 08:02, 1 August 2015 (UTC)
- Well, I think it's better than the one that was there, but I wonder if we can keep searching for an even better one. This one has the cinnamon back-lighted for the most part. I'd prefer a photo that had the light source in front or above so that one can really see the texture of the cinnamon stick, and perhaps show a little more of the bark, that is, not quite so close up. But I would leave this one there for now. Thanks! CorinneSD (talk) 18:46, 1 August 2015 (UTC)
- No-one has deleted an article, in my view; you basically moved material from existing articles to convert a redirect to an article, when there had already been extensive discussion about this topic. Peter coxhead (talk) 19:34, 4 August 2015 (UTC)
- Well, Stace (2010), New Flora of the British Isles, p.509 says of Cornaceae "fruit a drupe with 1 2-celled stone". So I guess not. But it's not clear to me that all botanical sources use the 'fruit categorization' terms in precisely the same way. Peter coxhead (talk) 11:28, 13 August 2015 (UTC)
- Picking up my last comment, I see that the Flora of China here says "Fruit a drupaceous berry", so it seems that you can take your pick. I'll ask at WT:PLANTS. Peter coxhead (talk) 14:41, 13 August 2015 (UTC)
- Judd et al say the fruit is a drupe. Heywood etal agree, but use the word "drupaceous". Is there a word "berryaceous"? That would cut us some slack. Plantsurfer 17:04, 13 August 2015 (UTC)
@Plantsurfer: by the way, in changing some Berry links to Berry (botany) I haven't been considering whether "berry" was correctly used in the first place, just what sense of "berry" was intended. Peter coxhead (talk) 14:34, 13 August 2015 (UTC)
- Yes, me too. Plantsurfer 17:08, 13 August 2015 (UTC)
An f. sp. example
It's become clear that a fungal race in pythopathology is kinda-sorta the same thing as forma specialis is mycology; it's principally the context that differs (the latter article even says so, pretty much). Are you aware of any case where mycologists have named a f. sp. (like Bandersnaticus frumiosus f. sp. carolli) and phytopathologists have designated the same population with a race name (e.g. race X3 of Bandersnaticus frumiosus), or vice versa? I think that would greatly help clarify at the Race (biology) article, at least in one field. And if there's a case of two+ races being classed as one f. sp., or vice versa, (i.e. if there may not always be a 1:1 correspondence), that would be important to factor in. All the literature I'm seeing clearly indicates (but does not spell out) that a mycologist is in a position to classify something as a f. sp. as a matter of biological nomenclature, while a phytopathologist is not (being a botanist of the host species), but may be in a better position to actually identify unique populations of the fungus to begin with, in applied work to develop resistant cultivars of the host plant, and whose IDed population might at some point be given a f. sp. name (that will probably not match the race name, since the former must be a Graeco-Latinism, and the latter is often just an alphanumeric code). — SMcCandlish ☺ ☏ ¢ ≽ʌⱷ҅ᴥⱷʌ≼ 11:55, 13 August 2015 (UTC)
- Well, I'm definitely not a mycologist – although I lead "fungus forays" in the autumn, I only use field guides. My impression is that you're on the right track, but I can't help you with the detail. User:Sminthopsis84 might know more.
- I've left the Race (biology) article aside for the present, though noting the real progress you've made. There's something of a mess created by splitting Berry and Berry (botany) to sort out – masses of existing links which may now go to the wrong article. Grumpy remark: being selected as the current "article for improvement" is no guarantee of improvement... Peter coxhead (talk) 14:31, 13 August 2015 (UTC)
- Speaking of such messes, see the genus merge stuff I posted to WT:FUNGI the other day. Just cleaning up one species has been a nightmare! You have my empathy as well as my sympathy. Anyway, are there any particularly recommendable botanical dictionaries/encyclopedias? I have and can otherwise get hold of plenty of general dictionaries of scientific jargon, but they end to lose too many nuances, and I've repeatedly notice people WP:GAMING definitions from them, on lot of articles, e.g. to apply an overbroad and imprecise definition in favor of a more narrow one in more topical, non-tertiary sources, or conversely to stick to a detailed definition that may be dated and not reflect current usage. — SMcCandlish ☺ ☏ ¢ ≽ʌⱷ҅ᴥⱷʌ≼ 15:35, 13 August 2015 (UTC)
- Hi User:SMcCandlish. I think you are seeing all types of literature that I am aware of. A factor that may be complicating things quite a lot is that many biologists refuse to dabble in nomenclature, and I think that explains them using race terminology. A plant pathologist and a mycologist are both permitted to apply the rules of nomenclature to establish a name, but many prefer not to. This may be because what they are studying is not something that they consider to be in itself a discovery. I expect that they also probably don't deal with very large numbers of organisms, so they aren't as acutely aware of the benefits of concise naming. So to summarize, I think you are right, that f. sp. simply provides a way to name a fungal pathogen race, the two are equivalent. It is rather a weird thing, that "informal" status of the f. sp., and for that reason I wondered if it was actually included in the latest code of nomenclature, but it is, and I think that probably means that it is here to stay, because matters to do with mycology have been thoroughly reworked by recent botanical congresses.
- I too have put the Race (biology) article aside for the present as a blood-pressure-defense mechanism, but have been planning to look in later. Sorry to see the massive mis-communication that has been going on there. It is very hard to deal with such complete misunderstanding of whatever one writes, as if one is trying to communicate with a different species. Sminthopsis84 (talk) 15:16, 13 August 2015 (UTC)
- Glad you were WP:JAGUARing; I'd meant to ping you and forgot. That one guy on that article (and the new sock who's arrived) are driving me nuts, but the solution seems to be to just keep adding sourced material until they have no argument left to make. I think this will be a months-long cleanup process. The landrace article needs similar work, and raises similar interference (not from the same party but from a different one who has also been active on both; there are basically three, not two, "camps"). — SMcCandlish ☺ ☏ ¢ ≽ʌⱷ҅ᴥⱷʌ≼ 15:35, 13 August 2015 (UTC)
- PS: I have to retroactively apologize for helping create some of the drama at that page. I let the Dunning-Kruger effect sneak up on me. My familiarity with the disuse of "race" in mammalology (and remembrance of being told by biologists when at university that it's avoided in that field, most especially by primatologists), combined with not having seen it used in caudatology in years, lead to an assumption that the term was also disused in other fields, so I argued that it was obsolete without checking my assumptions. I think that inspired some of the "delete this page!" stuff, inadvertently. I'm now committed to seeing the page done right. — SMcCandlish ☺ ☏ ¢ ≽ʌⱷ҅ᴥⱷʌ≼ 15:35, 13 August 2015 (UTC)
- @SMcCandlish: so you can see that we're both happy to leave you to it for the present, but don't hesitate to ask for assistance if there are new problems.
- Choosing my words carefully, as you will realize, I'm impressed by your example of calm reasonableness. :-) Peter coxhead (talk) 17:16, 13 August 2015 (UTC)