Talk:Botany

Template:Outline of knowledge coverage

Make this article better

What should be done next to make this article even better. It is currently rated "good".512bits (talk) 22:27, 1 June 2013 (UTC)

Hmm. It really isn't bad. I'd say that it is a bit confused about what organisms botany covers. Traditionally it included algae, fungi, and viruses, but much of the page is only about land plants. I'm not even sure what sources to look for, but a definite decision needs to be made about which if any algae to discuss (see Plant). The ecology section isn't great. I'm not sure what else to suggest, but having Autotroph as the main article for physiology of botanical organisms seems a bit perfunctory. Sminthopsis84 (talk) 18:37, 2 June 2013 (UTC)

I changed Autotroph to Plant physiology. I'll look at the ecology section next and then move to scope. When that's done is there a formal review process for improvement we can utilize? Thank you for helping. 512bits (talk) 01:43, 3 June 2013 (UTC)

Sorry, I don't know the answer to that, and wasn't able to find anything. It looks as if Wikipedia:Good article reassessment might have to be used as a first step, to check whether substantial changes are all good. I wonder if it is expected that you'd try to nominate it as a featured article, or if there is some other process. Sminthopsis84 (talk) 14:38, 3 June 2013 (UTC)

Modern, uptodate botany texts don't include algae, fungi, and bacteria, and I will update the article to that effect in a moment. I was looking for a "get ready for featured" type of review. Is there such a thing available? 512bits (talk) 23:22, 3 June 2013 (UTC)

No "get ready for featured" review exists. Peer reviews are extremely helpful for articles trying to get to GA status (which this article already has), but lessen their effectiveness for the Featured Article (FA) process (which is more rigorous and time-consuming for reviewers and editors). This article is certainly ready for a FA review, but its editors must be equally ready to continue improving it as the reviewers point out flaws. Send a message to my talk space if you think you'll have the time to participate in the FA review (it takes several weeks to complete).--MarshalN20 | ^Talk 01:25, 7 June 2013 (UTC)

I just did some improvements and I think we may be ready for the process. Perhaps take a shot at peer review anyway or just submit it to the featured process? 512bits (talk) 19:49, 8 June 2013 (UTC)

As a botany graduate who has spent a lifetime working in a University Botany department, I think this article reads like a first draft, is a bit of curate's egg. There is a lot that needs to be improved, but there are many redeeming features, and I hope you will forgive me for making some critical comments. They are intended to be constructive, so please don't feel bruised by them. I would encourage you to keep working on the weaker material for a while to bring it up to a professional standard. The overall structure seems fine, but in some places the language used appears naïve, as though written by a student who thinks they know what Botany is about but have no real background or experience in it. Sometimes the language is imprecise - what are plant population groups, for example? What is meant by chromosome counting - that is almost the botanical equivalent of accusing a banker of being preoccupied with cash-counting. So a good deal of copy editing still needs to be done bring the article up to the next level. The lead could be strengthened by a more accurate and current view of what botany and plant science are about, with more comprehensive linkage to what is already in Wikipedia. Botany today is very diverse - it includes, for example, paleobotany, plant evolution, Speciation, plant diversity, plant ecology, plant anatomy, plant cell biology (which includes chromosome counting and much else), cell signaling, plant biochemistry]], plant physiology, plant taxonomy, plant systematics, molecular genetics, genomics, proteomics, epigenetics, evolutionary developmental biology and systems biology, plant tissue culture and biotechnology. Note that the applied topics - Horticulture, Forestry, Agronomy etc. are not part of the core of Botany, but usually separated into separate University departments. Accordingly, the key scientists featured should be core botanists, and therefore, for all his merits, Norman Borlaug should not be included. There is no mention of many other botanists who were pivotal to the development of the subject in the last 200 years, e.g. Joseph Dalton Hooker, William Hooker, G. Ledyard Stebbins, Arthur Cronquist, Joseph Banks, Robert Brown, Arthur Tansley, and many of those plant explorers whose names are immortalized in the generic or specific names of plants, such as Joseph Banks, Tradescant, Bougainville, Poinsett, George Forrest, etc. There should be a link also to List of Botanists.

I suggest we take a week or so to review what is there and improve the weaker sections before submitting it for peer review. I am willing to do my part in this work, but it cannot be achieved overnight. Plantsurfer (talk) 11:22, 13 June 2013 (UTC)

Thank you for the comment. I think you and 512bits can probably do a better job at the FAC review as well, so please stay on board the process. Best wishes.--MarshalN20 | ^Talk 13:34, 13 June 2013 (UTC)

Thanks, will do!. Plantsurfer (talk) 21:23, 13 June 2013 (UTC)

Scientific disciplines

The article states "Botany covers a wide range of scientific disciplines including structure, growth, reproduction, metabolism, development, diseases, chemical properties, and evolutionary relationships among taxonomic groups." The itemized entities are topics, but not disciplines, and the discrepancy makes the article sound naff. How do you wish to deal with this? I suggest we give the disciplines their proper names. Plantsurfer (talk) 17:46, 14 June 2013 (UTC)

Actually the sentence is probably redundant, since the disciplines are itemized in the next paragraph. Plantsurfer (talk) 17:49, 14 June 2013 (UTC)

Notable botanists

Albert Blakeslee?? who he! OK, so the mud-wrestling begins. Clearly there could be endless competition for a place on the list for your favourite botanist. A short session of this might be quite entertaining and instructive, but I think in the end we need to define how big this list should be and what it is really for. It occurs to me that the average reader will see this as just a list of names, none of them meaning anything. So I suggest that the names need to be connected with a brief statement of their contribution to the subject. If that in its turn is to be prevented from degenerating into an endless list of contributions then we should try to limit it to 5 or 6 real milestones, pivotal moments in the development of the subject. One such might be the description of the Rhynie chert plants by Kidston and Lang. Another might be the first successful use by Don Grierson and his colleagues of molecular technology to construct a transgenic tomato containing an antisense pectinmethylesterase gene, marking the first successful experimental use of genetic engineering in plants. Another 20th century contributor of note was the late Paul Jarvis, FRS see http://bsbi.org.uk/PGJarvis.pdf whose work enabled measurement of water vapour and CO₂ fluxes from vegetation canopies. OK, just examples, but examples connected with identifiable step changes in understanding of the subject. I think that is what we need to do. Can we have some more suggestions please? Plantsurfer (talk) 20:02, 14 June 2013 (UTC)

I would suggest just to remove the section. For while we could come up with a guideline for notable botanists, this is bound to be controversial in bot the short and long-term. The simplest thing to do is to place the most remarkable individuals (who made a significant impact on the field) in the history section.--MarshalN20 | ^Talk 00:05, 15 June 2013 (UTC)

Botanical history

There seem to me to be two major omissions: first there is no mention of the origins of the major staple food cereals - or of the fact that their modern form is the result of selection from among wild ancestors. Second, the article majors on the pre-industrial history of botany, and almost completely omits the late 19th and early 20th century development of the subject, returning in the closing years with Arabidopsis and molecular genetics. That is an important omission and needs to be put right. Plantsurfer (talk) 16:27, 15 June 2013 (UTC)

I will help work on this.512bits (talk) 17:57, 15 June 2013 (UTC)

Great, thanks. Plantsurfer (talk) 18:10, 15 June 2013 (UTC)

It is probably best if we are not tripping over each other, and I need a break, so I will back off for a day or so to see how it goes. Plantsurfer (talk) 18:16, 15 June 2013 (UTC)

Introduction

The introduction needs a major re-write, particularly the last paragraph (which looks like a smurf convention). I volunteer to do that task, but first need for the other sections to be completed.--MarshalN20 | ^Talk 16:51, 15 June 2013 (UTC)

Agree, it was better two day ago. The intro should be a summary and that list of names isn't. Many of the other edits of the last two days are valid though and I'll help work through them. 512bits (talk) —Preceding undated comment added 17:53, 15 June 2013 (UTC)

I'm going to change it back. The intro should be written after the body is in stable solid form anyway.512bits (talk) 17:57, 15 June 2013 (UTC)

OK, it was weak before, but I accept the criticism. It has now become too much of a list. It would be helpful if other interested people could indicate where the other weak areas in the article now are. Plantsurfer (talk) 18:08, 15 June 2013 (UTC)

Now, plants have the more restricted definition of embryophytes ?

Under Botany#Scope and importance of botany, it says

"Now, plants have the more restricted definition of embryophytes ("land plants"), multicellular eukaryotic organisms that obtain their energy from sunlight by photosynthesis, and have life cycles with alternating haploid and diploid phases in which the sexual, haploid phase or gametophyte nurtures the developing embryo sporophyte within its tissues for at least part of its life."

I remember Plantæ as including the green algae, as the plant article is about.—Kelvinsong (talk)

See e.g. Plant Current definitions of Plantae. If we are talking of plants sensu stricto as land plants, their ancestors are charophytes, which are a separate division from chlorophytes. Re the evolutionary history, the great oxygenation event enabled the rise of Plantae, but was caused by cyanobacteria - Plantae were not responsible for it. Plants have caused or contributed to subsequent changes in oxygen concentration, for example during the Carboniferous period when the concentration reached about 30%. Plantsurfer (talk) 19:26, 15 June 2013 (UTC)

I think Charophyta still includes a small group of green algae. Still, I don't think it's a good idea to go against the definition used in the core Plant article. Consider rewording to something like

"Now, plants have the stricter definition of organisms descended from a photosynthetic green alga, and modern botany focuses on one particular clade (evolutionary branch? Readers may not know what a clade is.) of plant—the embryophytes, commonly referred to as the "land plants". ?

Also I think the part on alternation of generations in the definition should be removed or moved. 1 it is not unique to land plants, some algae also have it; 2 Very few readers are likely to understand (or even have heard of) the concept—it is not even mentioned in an honors high school biology course where I live. 3 it's likely to confuse even readers who know what Alternation of generations is—Angiosperms, etc. are sporophytes that shelter the gametophytes, not the other way around—Kelvinsong (talk) 20:36, 15 June 2013 (UTC)

Kelvinsong you are right that seed plant sporophytes shelter the gametophytes, but the fact is that their gametophytes nurture the next generation of sporophyte - i.e. the embryo, so that in seed plants there are three generations living together simultaneously. However, in their ancestors, liverworts let's say for example, gametophyte produces eggs in the archegonium and they are fertilized there to form a diploid zygote. The zygote develops into the sporophyte within the gametophyte's archegonium and is nurtured by gametophyte. That is the ancestral condition of all embryophytes. That is why they are called embryophytes. The situation in seed plants is a more complex and derived condition. What I said in the article is the right way round. Plantsurfer (talk) 21:35, 15 June 2013 (UTC)

Also Charophyte may informally be described as green algae, but they are not synonymous with the other group of green algae Chlorophyta. The two are now regarded as separate Divisions (equivalent to phyla). Charophytes contain the closest ancestors of embryophytes, and the closest of these are the Coleochaetales. These are regarded as closest to embryophytes because, among a raft of biochemical parallels, they are the first group to show signs of nurturing the earliest stages of multicellular development of their zygotes. Plantsurfer (talk) 21:57, 15 June 2013 (UTC)

This article explains it quite well. http://aob.oxfordjournals.org/content/103/7/999.abstract Plantsurfer (talk) 22:14, 15 June 2013 (UTC)

I've added that ref to the end of "The Charophyte class Charophyceae and the land plant sub-kingdom Embryophyta together form the monophyletic group or clade Streptophytina.[66]" in the Evolution section. It could well be used elsewhere also and that may not even be the best place for it. 512bits (talk) 10:51, 16 June 2013 (UTC)

Okay, I've added the following text to the article:

Now, plants have the stricter definition of organisms descended from a photosynthetic green alga, and modern botany focuses on one particular evolutionary branch of plant—the embryophytes, commonly referred to as the "land plants", which include seed plants (gymnosperms, the most well known being the pine trees, and flowering plants), ferns, and mosses. All embryophytes are multicellular eukaryotic organisms descended from an ancestor that obtained its energy from sunlight by photosynthesis, and have life cycles with alternating haploid and diploid phases. In embryophytes, the sexual haploid phase, or gametophyte, nurtures the developing embryo sporophyte within its tissues for at least part of its life, even in the seed plants, where the gametophyte itself is nurtured by another sporophyte.

—Kelvinsong (talk) 16:51, 16 June 2013 (UTC)

Who says that that this is the definition of plants or that modern botany focusses on embryophytes as opposed to, say, Viridiplantae? This seems to me to be unsourced and hence WP:OR. As one counter-example, the website of the Department of Plant Sciences of Cambridge University says "Plants are utterly fundamental to life on earth. From single-celled algae to the planet's largest living organism..." (see here). As another counter-example, the Department of Botany at the Smithsonian lists algae as one of its research areas here. A quick search for contents of "botany" and "plant science(s)" degrees in universities around the world suggests to me that algae are usually included. (One issue is that "botany" seems to be an old-fashioned term now, being replaced by "plant science" in the titles of most degrees and departments.) Peter coxhead (talk) 20:37, 16 June 2013 (UTC)

This is discussed in quite a balanced way in Embryophyte. Inevitably, research areas will overlap. Whether a University dept. chooses to teach a group or not is probably not relevant to the taxonomy. My Plant Science department taught fungi. so what?? Plantsurfer (talk) 21:03, 16 June 2013 (UTC)

You are right about Botany departments. Are there any left? Most plant scientists now flinch if you call them botanists. In my institution they would also flinch if you suggested they might be interested in agronomy or ecology. But the whole (multi)discipline is riddled with politics, contradictions and differences of opinion. Many plant scientists today work in large interdisciplinary groups with mathematicians, engineers, computational scientists, materials scientists etc. Pinning down what a botanist is in the modern world is not an easy matter. Worryingly (if you are a botanist) the majority of biologists seem to think that the boundaries between the traditional biological disciplines are increasingly irrelevant, made so by the unifying principles of molecular biology, which, they argue apply to all organisms. Plant/algae-orientated courses should merge into other molecular biology courses, for example. How would you defend botany against that argument? Plantsurfer (talk) 21:41, 16 June 2013 (UTC)

Yes, the discussion at Embryophyte#Phylogeny and classification is nicely balanced – but then as I wrote most of this section, I would say that. :-) My concern is that Botany#Scope and importance isn't balanced in the same way. There are competing definitions of "plant" and hence "botany"/"plant science" and these should be reflected in the article. Further, as you rightly note, the traditional biological disciplines are treated as increasingly irrelevant, something which is not made clear in the article.

I think I'm right in saying that there are now no degrees with the word "botany" in their title in the UK. Actually if you look at the content of biology degrees, whole organisms of any kind seem to be regarded as, at best, specialist final year topics. One consequence is that it's extremely difficult to find anyone in universities (at least in the UK) who can identify organisms or participate in taxonomic discussions once these move beyond molecular phylogeny. The museums still have such people, but for how much longer? "Serious amateurs" are now often the best people to ask if you want an organism identified. (End of grumpy old man rant!) Peter coxhead (talk) 22:20, 16 June 2013 (UTC)

I agree. Whole organism botany has been the domain of botanic gardens for some time. I think you need to get stuck into this article.
It appears to be rooted in some 19th century sepia-toned fantasy and 20th century approaches and milestones in the subject are poorly represented. Plantsurfer (talk) 22:40, 16 June 2013 (UTC)

"plant population groups"

What is meant by the phrase "plant population groups" in the lede? This is not only taxonomically vague but fails to specify what aspect is the focus of study - chemistry?? genetics?? ecology?? What information is this trying to convey? Plantsurfer (talk) 10:31, 16 June 2013 (UTC)

Probably a group of same species of plant, such as California poppies in a field, or an orchard of fig trees, etc. See [1] and [2]. 512bits (talk) 10:38, 16 June 2013 (UTC)

So why would that be a focus of botanical research as stated in the lede? It clearly is only one of a myriad of side-issue topics studied by botanists, and not a focus of botanical research generally. Plantsurfer (talk) 10:45, 16 June 2013 (UTC)

Don't know. I think that's been in the lede for ages. 512bits (talk) 11:06, 16 June 2013 (UTC)

OK, then what I suggest then is we change it to population biology which is a term that actually means something to professional botanists, and can be linked, and would be a credible focus of research. Whether it is actually one of THE most important focusses (?foci) of current botanical research I am not sure. Plantsurfer (talk) 11:21, 16 June 2013 (UTC)

Yep, done. 512bits (talk) 11:31, 16 June 2013 (UTC)

Can we please add molecular genetics to that list. Most modern botanists are precoccupied either with that or with molecular taxonomy/systematics. Plantsurfer (talk) 11:51, 16 June 2013 (UTC)

Yep, done.512bits (talk) 11:59, 16 June 2013 (UTC)

Fundamental life processes

"Botanical research has long had relevance to the understanding of fundamental biological processes other than just botany." a) botany isn't a life process b) processes such as? - provide some good examples. "Fundamental life processes such as cell division and protein synthesis can be studied using plants . . ." OK, an example, but a very weak one. c) plant cell structure and their processes of metabolism and cell division are both very different from those of animal cells. d) ". . . without the moral issues that come with conducting studies upon animals or humans." sounds like wp:or. Sources? e)Is this implying that plant cells are somehow an ethical model cell? If so I say this is false. Most studies of animal cell cycles, etc. would be carried out ethically using cultured animal cells, (see HeLa, just for example, but please, don't come back to me with reasons not to use this cell line) not plant cells, which are too fundamentally different in their structure and physiology. If you hope to learn about muscle cells using a plant cell model, good luck! Plantsurfer (talk) 14:18, 16 June 2013 (UTC)

Evolution

"After the evolution of xylem and phloem during the Silurian and Devonian periods, vascular plants developed along two lines: vascular cryptogams which reproduce by spores and evolved first, and spermatophytes, which reproduce by seed." This is ambiguous and misleading. It suggests that two lineages reached different evolutionary end-points or stages. Actually, there were several lineages of vascular cryptogams which reproduced by spores, and several of htose lineages evolved seeds. For example, the late Devonian and Carboniferous lycopods evolved megaspory and seeds totally independently of the Progymnosperms and seed ferns. Plantsurfer (talk) 00:08, 17 June 2013 (UTC)

Gymnosperm monophyly

After looking into this more, it seems the confusion with this gymnosperm monophyly thing originates from the fossil gymnosperms. Campbell-Reece Biology from 2008-ish states that all surviving gymnosperms are monophyletic, as does the most recent (2011) source on the Gymnosperm page

It says

Although the extant taxa are clearly monophyletic, their relationships to the numerous and diverse groups of fossil gymnosperms remain obscure and incompletely understood.

I think it depends on whether you count fossil groups like Bennettitales as gymnosperms; the textbook says no, the Bennettitales article says yes. As it stands though, the current article text gives the impression that a pine tree somehow evolved into an angiosperm.—Kelvinsong (talk) 14:31, 18 June 2013 (UTC)

I think this is exactly correct. Although it can't be regarded as totally settled, the extant gymnosperms appear to form a clade, according to recent research. However, there are clearly extinct members of the pan-spermatophytes (in the sense of Cantino et al. 2007) which do not belong to any of the extant groups of gymnosperms. Some of these, like Aneurophyton, have traditionally been treated as the paraphyletic group "progymnosperms", but others, like the pteridosperms or seed ferns have traditionally been treated as gymnosperms. Since molecular studies can't be done on these extinct groups, their position in the phylogenetic tree will always be in doubt. (Most sources I've looked at put the Bennittatales firmly in the gymnosperms.)

Perhaps the safest thing to say is that following the evolution of true seeds, seed plants diversified, giving rise to a number of extinct groups as well as the extant gymnosperms and the angiosperms. Peter coxhead (talk) 16:39, 18 June 2013 (UTC)

Yes that makes a lot of sense.Plantsurfer (talk) 17:11, 18 June 2013 (UTC)

Ok, I've now re-written that bit along the lines I suggested above. The text still doesn't quite deal with the point that you (Plantsurfer) made above re seed-like structures occurring outside the line leading to spermatophytes. Peter coxhead (talk) 22:30, 18 June 2013 (UTC)

what I want to say is something like the following. Any suggestions how to condense it further:

Vascular cryptogams, plants with true xylem and phloem that reproduced by spores that germinated into free-living autotrophic gametophytes, evolved during the Silurian period and diversified into several lineages during the late Silurian and early Devonian. By the end of the Devonian period, several groups, including the lycopods, sphenophylls and progymnosperms, had evolved megaspory independently and their reduced gametophytes developed within the sporangia of the sporophyte, a condition known as endospory. These developments were early experiments in reproduction using seeds, which was most successfully developed in the progymnosperms and their descendents, the seed ferns, the extinct ancestors of modern spermatophytes. Plantsurfer (talk) 23:41, 18 June 2013 (UTC)

It's all very tricky to word in a short paragraph, while retaining the nuances of reliable sources. To quote from Taylor et al. (Paleobotany, 2009): "Many regard the origin of the seed habit as the end member of a logical progression that began with homospory, was followed by various forms of heterospory ... and culminated in the structure termed the seed ... however, there is no a priori reason that the seed habit could not have evolved directly from a homosporous system". The original includes references supporting both positions, whereas your last sentence implies a direct line ("early experiments", progymnosperms as the direct ancestors of modern spermatophytes, whereas they may be side branches). An entire chapter (13) in Taylor et al. is devoted to detailed discussion of the evolution of the "seed habit". Breaking down what you wrote (and removing some jargon), here's my version:

• Plants with true xylem and phloem that reproduced by spores germinating into free-living gametophytes evolved during the Silurian period and diversified into several lineages during the late Silurian and early Devonian.
• By the end of the Devonian period, several groups, including the lycopods, sphenophylls and progymnosperms, had independently evolved "megaspory" – their spores were of two distinct sizes, microspores and megaspores. Their reduced gametophytes developed from megaspores retained within the spore-producing organs (megasporangia) of the sporophyte, a condition known as endospory.
• A "true" seed consists of a megasporangium surrounded by one or two sheathing layers (integuments). The young sporophyte develops within the seed, which splits to release it. The earliest known true seeds date from the Middle Devonian. Following the evolution of the seed habit, plants with seeds diversified, giving rise to a number of extinct groups, including seed ferns, as well as the modern gymnosperms and angiosperms.

I think this is as accurate as it can be in the space, and it's all sourceable (e.g. to Taylor et al.) What do you think? Peter coxhead (talk) 08:45, 19 June 2013 (UTC)

Nice. I think that looks very good and provides quite enough information for the purpose of this article. Plantsurfer (talk) 12:40, 19 June 2013 (UTC)

Status check

Sorry I haven't been around for a few days. I'm sort of lost trying to sieve through all the above comments. Where are we at with this and what do we still need to do? 512bits (talk) 02:47, 21 June 2013 (UTC)

Improvements have been made, it's getting there certainly, but there is a way to go yet before this is a credible FA. I am going to be blunt: Parts of it, including the lede, still come across as an essay written by someone who is not quite in touch with the topic.

Lede "In the 19th and 20th centuries, major new techniques were developed for studying plants, including microscopy" - Contributions to botanical microscopy began with Hooke's Micrographia 2 centuries before. Developments in 20th century microscopy can be split into 2 broad areas Optical microscopy and electron microscopy each of which made significant contributions in 20th century botany.

Cut it from lede. 512bits (talk) 11:10, 23 June 2013 (UTC)

Lede paragraph 4: sentence 1 essentially repeats the first sentence in paragraph 2, and is therefore redundant.

I changed that. I hope it's better. 512bits (talk) 02:11, 23 June 2013 (UTC)

History: I remain disturbed by scope/balance of this history section, its subheadings and other aspects. It is too heavy on mediaeval botany and skips most of 20th century development. The reverse balance would be more appropriate. I could accept the subheader title "Early modern botany" for 20th century botany, but not for 15th century. The first 2 paragraphs could be moved into Early botany, and the modern botany section needs significant amplification and strengthening.

Made some changes. 512bits (talk) 23:50, 25 June 2013 (UTC)

Scope and importance - This starts off "Botanists study...." blah di blah. Haven't we already covered all that? For me this section comes across as surprisingly confused and directionless. The importance of Botany to mankind is that we and the existence of the biosphere generally are underpinned by the solar energy captured by photosynthesizing organisms. We study plants because it is vital to understand how they function in earth environments, what drives their diversity and whether it is necessary for the functioning of the biosphere, because if we should inadvertently destroy them we are all so dead. We need to get some of that importance and excitement across to a readership that mostly view plants as tedious background. So the section should lead with paragraph 2and Human nutrition.

Made some changes. 512bits (talk) 23:50, 25 June 2013 (UTC)

Fundamental life processes - see my earlier remarks. The second sentence just doesn't stand up to scrutiny.

I cut this. 512bits (talk) 02:11, 23 June 2013 (UTC)

Environmental changes - the title is wrong. Why would that topic be included here? It needs to justify its inclusion in a summary of botany, and it comes across as weak, naïve.

Plant ecology - OK we need to say something about this, because we all know it is vital to the understanding of plant functioning in their natural habitats, but this text wastes time defining e.g. biomes. We need to lift the section above that basic high school ecology (which is after all the scope of another article) to focus exclusively on what we want to say about Plant Ecology.

Evolution - is good

Plant physiology - is weak. Full of platitudes, lacking real information and substance. This subsection of botany was the stuff of most of 20th century endeavour that needs to be reflected here. Where are plant growth regulators, e.g.? The section needs to identify what are the key issues and developments in modern plant physiology and summarize them. Plantsurfer (talk) 11:29, 21 June 2013 (UTC)

I agree with Plantsurfer. What I would add is that this kind of article is significantly more difficult to write in my experience than are specialized subarticles (e.g. a separate article on plant ecology) because of the need to be accurate but yet succinct. Maybe we can work together on some parts, as we did above on some evolutionary issues? Peter coxhead (talk) 13:39, 22 June 2013 (UTC)

Sure. I'll do what I can to be helpful. Thanks everyone for working as a team. 512bits (talk) 02:11, 23 June 2013 (UTC)

"Key scientists in the history of botany include Theophrastus, Ibn al-Baitar, Carl Linnaeus, Gregor Mendel, and Norman Borlaug." C'mon, we can do better than this! Why does Borlaug (an Agronomist) rate inclusion among these giants. Are there no true botanists to represent 20th/21st century botany?? Plantsurfer (talk) 10:40, 23 June 2013 (UTC)

How about Luther Burbank, Barbara McClintock? I would also like to include in that list someone from the Far East, but my knowledge of botanists from that region, sadly, isn't what it should be. 512bits (talk) 11:08, 23 June 2013 (UTC)

Proposed revision of lede

I am proposing the following edit of the lede. Purpose is to improve logical flow and indicate better where botany came from. Comments on a postcard please

Botany, plant science(s), or plant biology (from Ancient Greek βοτάνη botane, "pasture, grass, or fodder" and that from βόσκειν boskein, "to feed or to graze"), is the science of plant life and a discipline of biology. A person engaged in the study of botany is called a botanist.

Botany began in prehistory as herbalism with early human efforts to identify, and later to cultivate, edible, medicinal and poisonous plants, making it one of the oldest branches of science. Nowadays, botanists study about 400,000 species of living organisms. The spice trade was of great economic and political importance during the Middle ages, driving world exploration. Medieval Physic gardens, such as those of University of Oxford Botanic Garden (founded 1632) and Royal Botanic Garden Edinburgh (founded 1670) collected plants of medical importance, and the efforts to catalogue and describe their collections were the beginnings of plant taxonomy which led to the binomial system of Carl Linnaeus in 1753. In the 19th and 20th centuries, major new techniques were developed for the study of plants, including microscopy, analysis of chromosome number, plant chemistry and live cell imaging. In the last two decades of the 20th century, plant genetic analysis exploited the new disciplines of genomics and proteomics and DNA sequences were used to classify plants more accurately.

Modern Botany covers a wide range of scientific disciplines including the study of plant structure, growth, reproduction, metabolism, development, diseases, chemical properties, evolutionary relationships, systematics, and plant taxonomy. NOTE - these are topics, ok, but not disciplines. Can we please get the wording right and properly link

Traditionally, the science of botany also included the study of fungi, algae but this has become less common. Because Tobacco mosaic virus was the first virus to be discovered, virology was originally studied by botanists.

Key scientists in the history of botany include Theophrastus, Ibn al-Baitar, Carl Linnaeus, Gregor Mendel, and Norman Borlaug.

Plantsurfer (talk) 11:30, 23 June 2013 (UTC)

I agree the lede needs work and overall your proposal is better, but I have some suggestions:

• • A lede should be a summary of the body and as such we should work it last, after we feel the article is where we want it
  • As a summary, there should be no footnotes in the lede, they should be in the body where the supporting info lies (the current lede has that problem too)
  • Replace Borlaug with McClintock
  • Cut "A person engaged in the study of botany is called a botanist", it's rather obvious
  • We should end up with 3-4 paragraphs of 4 or so sentences each
  • The history paragraph is good but might be a bit too long, not sure
  • Merge what are currently the last two paragraphs (virus and notables)
  • I've copied the history and modern botany ("b" should be lower case) to the current article.
    • Just my thoughts. 512bits (talk) 11:57, 23 June 2013 (UTC)

McClintock is good. Any more? It would be good to have representatives of a couple more key areas of the subject. Might I suggestKatherine Esau for Plant Anatomy? Plantsurfer (talk) 13:22, 23 June 2013 (UTC)

I agree with 512bits that the lead is the last thing we need to work on. We first need a stable article body.--MarshalN20 | ^Talk 15:21, 23 June 2013 (UTC)

Proposed revision of Plant ecology section

==Plant ecology==

Plant ecology describes the ways plants relate to and function in their habitats, the environments in which they complete their life cycles. Plants depend upon certain edaphic (soil) and climatic factors in their environment but may also modify these factors by e.g. decreasing albedo, increasing interception of runoff and stabilization of soils.

Plants compete with other organisms in their ecosystem for resources. They interact with their neighbours at a variety of spatial scales in groups, populations and communities that collectively constitute vegetation. Biomes such as tundra and tropical rainforest, are regions with similar abiotic and biotic factors, climate, and geography with characteristic dominant plants.

Plant ecologists study the composition of local and regional flora, the biodiversity, genetic diversity, fitness and adaptation of plants to their environment and their competition with other species.

Herbivores eat plants, but plants can also defend themselves and some species are parasitic or even carnivorous. Other organisms form mutually beneficial relationships with plants. For example mycorrhizal fungi provide plants with nutrients, ants are recruited by ant plants to provide protection, honey bees and other pollinators pollinate flowers, and dispersal vectors distribute spores and seeds.

===Plants, climate and environmental change===

Plant responses to climate and other environmental changes can inform our understanding of how these changes affect ecosystem function and productivity. For example, plant phenology can be a useful proxy for temperature in historical climatology, and for indicating the biological impact of climate change and global warming. Palynology, the analysis of fossil pollen deposits in sediments from thousands or millions of years ago allows the reconstruction of past climates. Estimates of atmospheric CO₂ concentrations since the Palaeozoic have been obtained from stomatal densities and leaf shapes of ancient land plants. Ozone depletion can expose plants to higher levels of ultraviolet radiation-B (UV-B), resulting in lower growth rates. Moreover, plant systematics and taxonomy are essential to understanding habitat destruction and species extinction.

Plantsurfer (talk) 18:39, 23 June 2013 (UTC)

Yes, I think this is a good improvement. I like the fact that it places the climate with greater prominence in the section.--MarshalN20 | ^Talk 19:14, 23 June 2013 (UTC)

Support, made a few small changes—Kelvinsong (talk) 20:17, 23 June 2013 (UTC)

Thanks, OK I'll make the change. Plantsurfer (talk) 20:50, 23 June 2013 (UTC)

Notable Botanists Removal Challenge

Per the short discussion above (on "Notable botanists"), the best way to slowly do away with the list is to insert the names already in it inside the relevant article sections. I will start by doing away with the two Greek people that are prominently featured in "Early botany". I won't remove the Muslim people (also in the aforementioned section) because more is still needed to be known about them and their work (in the section).--MarshalN20 | ^Talk 21:01, 23 June 2013 (UTC)

I took care of this. 512bits (talk) 00:34, 27 June 2013 (UTC)

Plea for Biochemistry

I have just rattled this off—perhaps it could be hacked as the basis of a section. Probably does not need much more than this othere than a bit of linkage to topics and to notable contributors. Might also mention the relationship of this to the modern approach of metabolomics:

Plant biochemistry studies the chemical processes used by plants in their general or primary metabolism including, for example, the Calvin cycle and Crassulacean acid metabolism used in photosynthesis, and in the synthesis during growth of the specialized materials used in their construction, such as cellulose, lignin and cutin. Biochemistry also includes plant secondary metabolism, which is responsible for the production of many commercially valuable plant products such as the carnauba wax from Copernicia cerifera, rubber, spices (e.g. capsaicin), aromatic compounds such as essential oils, toxic compounds such as the alkaloid coniine from hemlock and opium from opium poppies. Plants also synthesize coloured dyes and pigments such as the anthocyanins and indoxyl, source of the blue dye indigo used traditionally used to dye denim. In modern plant science, biochemistry is just one of a suite of related molecular-scale biological disciplines, including genetics, molecular biology, genomics, proteomics and metabolomics, which may in turn be studied using computer modeling and informatics. Plantsurfer (talk) 14:16, 24 June 2013 (UTC)

...Is that one sentence? :)—Kelvinsong (talk) 14:30, 24 June 2013 (UTC)

...Yes, sorry :) Easily broken up however, as above. The last sentence is OR of course, but I believe it to be broadly true, and the Biochemistry article says something analogous. It is unlikely to be too difficult to find sources to support it. Also my apologies to those allergic to smurfs. Plantsurfer (talk) 15:23, 24 June 2013 (UTC)

It would be worth emphasizing that plant biochemistry is largely the product of 20th century plant science, driven by 20th century understanding of Chemistry and the new technologies available for chemical analysis (spectroscopy, chromatography, etc.)Plantsurfer (talk) 15:32, 24 June 2013 (UTC)

I vote for cutting the last sentence, throwing in some solid references, and adding to article. 512bits (talk) 00:07, 25 June 2013 (UTC)

OK. I presume the biochem bit is to go into Modern botany? Can we put it in there now so we can see things shaping up? Refs can follow. Plantsurfer (talk) 10:31, 26 June 2013 (UTC)

Sequence is important - the new bit on Biogeog. etc should come early, because developments there date from the very early part of the century. Odum was a great ecologist, and many people will see him as a founder of the subject, but the foundations of the concepts of plant community and succession came 15 years before he was born, with the work of HC Coles (1899)a,b,c,d The ecological relations of the vegetation on the sand dunes of Lake Michigan. Parts 1-4. Botanical Gazette, 27, 95-117, 167-202, 281-308, 361-391. He used the word succession in the title of his paper Cowles, H.C (1910) The fundamental causes of successions among plant associations. Report of the British Association for the Advancement of Science 1909, 668-670. Note "plant associations". The idea that plant communities changed progressively (we call this succession or vegetation change today, (see e.g. book by Colin Burrows isbn 0-04-580013-8) towards a climax was already well developed by the time of Odum's birth, the climax concept expressed by Clements F (1916) Plant succession: an analysis of the development of vegetation. Carnegie Institute Washington publication no. 242; Clements FE (1928) Plant succession and indicators. Wilson, New York; Clements FE (1936) Nature and structure of the climax. Journal of Ecology 24, 252-284. At the same time (1916-1939) AG Tansley had a major input to these ideas, and they were put to the test at the observational level by the work of WS Cooper (early 1920's to late 1930's) on plant succession on the moraines of retreating glaciers at Glacier Bay, Alaska. So ... my point is that Odum is a secondary source, and the foundations laid by these four pioneers of 20th C plant ecology need to be acknowledged. Plantsurfer (talk) 10:31, 26 June 2013 (UTC)

Now to return to the topic of Katherine Esau. That article correctly states "Esau was a pioneering plant anatomist—perhaps the greatest plant anatomist of the 20th century. Her books Plant Anatomy and Anatomy of Seed Plants have been key plant structural biology texts for four decades." Spot on. Her achievement was huge, and her contribution remains the foundation stone of plant developmental research today. In my view she has to be mentioned in the Modern botany section. Plantsurfer (talk) 10:31, 26 June 2013 (UTC)

The construction "One of the more urgent unanswered botanical questions ..." is WP:editorializing and needs to phrased more objectively. Also, some of these things are not unanswered questions, they are topics of intense, active research. see e.g.Reay, D., Dentener, F., Smith, P., Grace, J. and Feely, R.A. (2008) Global nitrogen deposition and carbon sinks, Nature geoscience 1(7) p.430-437 doi:10.1038/ngeo230 Korbetis, M., Reay, D. and Grace, J. (2006) New directions: Rich in CO2, Atmospheric environment 40(17) p.3219-3220 doi:10.1016/j.atmosenv.2006.01.032 Grace, J., Meir, P. and Malhi, Y. (2001) Keeping track of carbon flows between biosphere and atmosphere., Ecology: Achievements and Challenges, p.249-269 Geider, R.J., Delucia, E.H., Falkowski, P.G., Finzi, A.C., Grime, J.P., Grace, J., Kana, T.M., La Roche, J., Long, S.P., Osborne, B.A., Platt, T., Prentice, I.C., Raven, J.A., Schlesinger, W.H., Smetacek, V., Stuart, V., Sathyendranath, S., Thomas, R.B., Vogelmann, T.C., Williams, P. and Woodward, F.I. (2001) Primary productivity of planet earth: biological determinants and physical constraints in terrestrial and aquatic habitats, Global change biology 7(8) p.849-882 Plantsurfer (talk) 10:31, 26 June 2013 (UTC)

Particularly since the mid-1960s, new understanding of plant physiology - water transport, physics of evapotranspiration and molecular diffusion, methods of measuring stomatal aperture, transpiration and rate of photosynthesis enabled precise description of the rates of gas exchange between plants and the atmosphere. These developments are very considerably the result of work by pioneers such as Monteith, Paul G Jarvis, Graham D Farquhar, John Grace, and underpin modern attempts to measure and model plant productivity and their contribution to the regional and global carbon and water cycles. Plantsurfer (talk) 10:31, 26 June 2013 (UTC)

Here it would also be desirable to make a sentence on the colossal contribution to plant science (biological sciences generally) by the new statistics being developed by Ronald Fisher and Frank Yates. Dawkins called Fisher the greatest biologist since Darwin. Their contributions made rational experimental design and analysis possible. Plantsurfer (talk) 10:31, 26 June 2013 (UTC)

I suppose it is a no-brainer that biogeography dis not become possible until there was some kind of world view of plant distributions. The spice trade, etc. and the efforts of plant explorers such as Cook laid foundations prior to 20thC. Who are the key modern contributors? People like Eric Hultén undoubtedly. see e.g. Hultén, Eric (1958) The Amphi-atlantic plants and their phytogeographical connections. Kungl. Svenska vetenskapsakademiens handlingar, 4:7:1: 340 pp. Stockholm, Almqvist & Wiksell. and other publications cited by the article on him. Then perhaps Nicholas Polunin (1960) Introduction to plant Geography. Longmans and his brother Oleg Polunin. Holdrige of Holdridge life zones fame, who summarized the relationship between climate and climax vegetation (miserable stub article that needs major development, but later). Plantsurfer (talk) 11:19, 26 June 2013 (UTC)

Neolithic founder crops

The modern forms of the major staple foods, such as bananas and plantains maize and other cereal grasses and pulses, as well as flax and cotton grown for their fibres, is the outcome of prehistoric selection over thousands of years from among wild ancestral pants with the most desirable characteristics. Plantsurfer (talk) 17:21, 26 June 2013 (UTC)

Is that what you wanted 512bits? Plantsurfer (talk) 17:21, 26 June 2013 (UTC)

Very nice. I'll stick this in "Human nutrition". 512bits (talk) 23:25, 26 June 2013 (UTC)

Difficult to pick out page numbers in Zohary & Hopf. The entire book is a masterwork on the topic, with chapters on individual founder crop categories. However, the bones of the point seem covered by the following statements: page 20 "the first definite signs of wheat and barley domestication appeared in the Fertile Crescent in the second half of the eleventh millennium cal (sic) BC." and p22 "several traits that characterize domesticated cereals (the domestication syndrome) seem to be the outcome of conscious or unconscious selection under domestication" (followed by list of such traits -erect plants, synchronous tillering and seed production, seed size, seed number, etc.) In Stover and Simmonds there is discussion of human selection of bananas on pages 106 through 126. Plantsurfer (talk) 10:43, 27 June 2013 (UTC)

I added the page numbers. 512bits (talk) 23:05, 28 June 2013 (UTC)

Cladistics??

In the Systematics section, would it be appropriate do you think to make reference to cladistics? Plantsurfer (talk) 12:36, 27 June 2013 (UTC)

Other missing items that occur to me are 20th C understanding of Plant Growth Regulators and micropropagation/plant tissue culture pioneered by Frederick Campion Steward, including the concepts that plant cells are totipotent and that they can now be genetically modified to produce useful products in vitro. Also, that these biotechnologies have facilitated molecular genetics and GM. Are there others that you have spotted? Plantsurfer (talk) 12:46, 27 June 2013 (UTC)

I have made a number of changes to section sequence, and have re-located some paragraphs to other sections, largely conservatively. I have also added some bits to modern botany. My feeling about that section was that it has needed a kind of sub-lede, and I have tried to provide that. I am coming close to the point where my concerns about the article have been addressed (although, no doubt some refs and tidying still need to be done). What are the feelings of you all about the way it looks now, and where do you see the need for change and further development before it can go for FA. ?? Plantsurfer (talk) 13:43, 27 June 2013 (UTC)

Early modern botany

OK, it is clear after leaving the article to digest for maybe an hour or two, that the Early modern botany section is not complete yet. No mention of Goethe. His ideas, expressed in Metamorphosis of Plants on the homology of leaves and other floral organs were prescient. The orphan sentence on the discovery of the nucleus sticks out like a ..., like a.. whatever. It needs addition of other contributions to cell biology from people like Hugo von Mohl and De Bary. These guys laid the foundations of the 20th century anatomy of Esau. Plantsurfer (talk) 21:42, 27 June 2013 (UTC)

Important to us, but the history sections take up a big portion of the article. Most readers will get lost with so much detail. What do others think?512bits (talk) 23:15, 28 June 2013 (UTC)

I think we should write it in, and then subject the entire article to brief, (please), but rigorous précis, with the aim of removing all verbiage that doesn't earn/justify its space. Plantsurfer (talk) 23:52, 28 June 2013 (UTC)

The History of botany article is what covers (or should cover) all notable subjects pertaining to the history of botany.

Our task is more difficult. We have to (basically) select those who are obviously the most important figures in terms of their contributions to the field.

For instance, on the "three German fathers of Botany", none (currently) seem important enough to be in this article. For them to stay, there should be a clear explanation as to how their work impacted botany. I mean, (hypothetically) I can also go outside and make my own original observations on plants. I guess the question you must answer (for all the people mentioned in the history section) is "So What?" (Why are they and their contributions relevant?)

And I'm not just picking on the Germans. The Golden Age Muslims also currently seem irrelevant. I don't even know why it is relevant to mention their woks.

Yes, I admit to being a complete ignorant on the history of botany; but so are most people. Your job as Feature Article editors is to eliminate ignorance. ;)--MarshalN20 | ^Talk 23:29, 28 June 2013 (UTC)

I would vote for keeping the Germans in, perhaps expand a bit, but if others want them cut, ok. I think I added or expanded the Muslim people. My part was to make the article less European-centric.512bits (talk) 11:21, 29 June 2013 (UTC)

Wrap up items

I think this is now quite sound. I made some tweaks. Some remaining items: 1) the intro para of Plant biochem sections needs refs. Which ones did you use to write it? 2) last para of Plant ecology needs refs 3) make the lede a nice abstract of the article 4) After the above three are fixed we submit to peer review or for feature status as MarshalN20 mentioned, how do we do that?

512bits (talk) 23:21, 28 June 2013 (UTC)

OK, I'll try to fix some of this over the weekend. Plantsurfer (talk) 23:54, 28 June 2013 (UTC)

Hi 512bits The following book could be used as the source for all of this:

P.M. Dey and J.B. Harborne (eds.) 1997. Plant Biochemistry. Elsevier Ltd. ISBN: 978-0-12-214674-9

More specifically, its chapters could be used as follows

"Plant biochemistry studies the chemical processes used by plants in their general or primary metabolism including the Calvin cycle and Crassulacean acid metabolism used in photosynthesis," Chapter 2 - Photosynthesis , pp. 49-110, J.R. Bowyer, R.C. Leegood

", and in the synthesis during growth of the specialized materials used in their construction, such as cellulose," Chapter 5 - Carbohydrate metabolism: Structural carbohydrates, Pages 205-236, J.S.G. Reid lignin. Chapter 10 - Phenolic metabolism, pp. 387-416, D. Strack

"Biochemistry includes plant secondary metabolism, which is responsible for the production of many commercially valuable plant products such as the carnauba wax from Copernicia cerifera, rubber," Chapter 6 - Plant lipid metabolism, pp. 237-272, J.L. Harwood

spices (e.g. capsaicin), aromatic compounds such as essential oils, toxic compounds such as the alkaloid coniine from hemlock and opium from opium poppies." Chapter 12 - Special nitrogen metabolism, pp. 439-486, M. Wink

"Plants also synthesize coloured dyes and pigments such as the anthocyanins and indoxyl, source of the blue dye indigo used traditionally used to dye denim." Chapter 10 - Phenolic metabolism, pp. 387-416, D. Strack Plantsurfer (talk) 12:35, 30 June 2013 (UTC)

Chlamydomonas reinhardtii as a model organism for plants?

Under Genetics, the article includes:

A green alga, Chlamydomonas reinhardtii, is a model organism that has proven important in advancing knowledge of cell biology.

Now I recall a big discussion about what counts as a plant, and looking at Botany#Scope and importance, it looks like the embryophyte definition won (I know, I know). So why are we including C reinhartii, a unicellular green alga, and a chlorophyte on top of that. C reinhardtii is useful because it has green chloroplasts like the embryophytes, but it's probably confusing to mention a "nonplant" as a model organism for plants.—Love, Kelvinsong talk 01:04, 29 June 2013 (UTC)

If it looks like embryophyte "won", this is wrong. The set of organisms put under the title "botany" (itself rapidly becoming an obsolete term) varies from source to source. Green algae are often included. However, I agree that if this species is used here, some comment or qualification is needed. Peter coxhead (talk) 08:47, 29 June 2013 (UTC)

Agree, I think Kelvin should make his proposed changes. 512bits (talk) 11:17, 29 June 2013 (UTC)

Agree, over to you Kelvinsong Plantsurfer (talk) 16:24, 29 June 2013 (UTC)

I will add the following text to the article if there's no objections:

While not an embryophyte itself, the single celled green alga Chlamydomonas reinhardtii has proven useful for study in some areas of plant cell biology because its cell is similar in some ways to those of plants—for example it contains a green-pigmented chloroplast related to the green chloroplasts in plants.

I also want to add the following (which I know from working on Chloroplast), but I don't know where to find specific references for it:

However, to obtain a better picture of plant cell biology, cells of land plants like spinach, Arabidopsis, and corn are also often studied.

—Love, Kelvinsong talk 16:39, 29 June 2013 (UTC)

C. reinhardtii is both an older model organism and a current plant model organism. It was used extensively for studies of photosynthesis (light reactions and carbon concentration mechanisms), and flagellar movement (motors) in green plants in general, then for cell growth, and cell cycle regulation. It is now being used for bioengineering to create plant recombinant proteins in its chloroplasts. A couple of ISBNs that I found in google book searches: 978-1-4419-7347-4, ISBN-13: 978-1560229995; it is considered a much safer factory than higher plants, it grows quickly, cheaply, and abundantly, plus there is lots of current information available and plenty of gene sequencing tools. It has some mutations that allow the study of certain types of processes in higher plants, also, such as nitrite and nitrate pathways. It should be mentioned as a primary model organism in botany. --AfadsBad (talk) 20:01, 29 June 2013 (UTC)

No question at all that C. reinhardtii is a notable model organism for cell and molecular biology. Probably there is stuff that botanists can learn from it, but the same goes for many other organisms that we can't list here - see for example Model organism#Protists and Model organism#Plants. This article is no place to discuss the model organism credentials of C. reinhardtii. I vote to leave it out on the grounds that we have to draw a line somewhere, and for me that line is at multicellularity. C. r. doesn't have it. If there is strong feeling for mentioning C. r. at all, then its contribution to understanding of plants must be very clear. At present the sentence reads "A green alga, Chlamydomonas reinhardtii, is a model organism that has proven important in advancing knowledge of cell biology." Sorry, cell biology? - that's another article. Plantsurfer (talk) 11:09, 30 June 2013 (UTC)

Agree with Plantsurfer, this should be left out and the topic cut out.512bits (talk) 11:33, 30 June 2013 (UTC)

So…no Chlamydomonas reinhardtii at all? (And I just learned how to spell its name! ;) )—Love, Kelvinsong talk 13:35, 30 June 2013 (UTC)

Sorry, my point was not clear. I think that it should stay, but that its contribution to understanding of plants should be succinctly stated. The current statement that it advances knowledge of cell biology is inadequate. Since you know about photosynthesis, you are probably the best person for the job. Oh, and a relevant source. Plantsurfer (talk) 13:45, 30 June 2013 (UTC)

Well, most plant specific chloroplast stuff comes from study of "real" plants like spinach, Arabidopsis, and corn. I think the algae like CyazonadanblahCyanidioschyzon merolæ (? What is it with algal names?) and Chlamydomonas reinhardtii are used for more "basal" chloroplast functions/features like ctDNA ^{[I have a reference but it doesn't have a doi, and I'm too lazy to write a full citation]}, photosynthesis, and chloroplast division (but often along with real plants like peas, soybeans, etc.) Chlamydomonas reinhardtii is used for example to study starch synthesis [3].—Love, Kelvinsong talk 14:10, 30 June 2013 (UTC)

Yes, the current sentence is worthless; I think that the most important thing for botany may be plastid reproduction specifically, but it may be photosynthesis in general. Someone would have to research it. For now, though, that particular sentence should not be in the article--my opinion. --AfadsBad (talk) 14:40, 30 June 2013 (UTC)

Well if we're going to go into chloroplast division, that's going to stray even more off topic cause that was worked out thanks to studying Cyanidioschyzon merolæ, a red alga (along with spinach and Arabidopsis). See [4] for a good review on the topic.—Love, Kelvinsong talk 15:54, 30 June 2013 (UTC)

New text?

A variety of model organisms are useful for studying plant cell biology and the chloroplast. Corn has been used to study mechanisms of photosynthesis and phloem loading of sugar in C₄ plants. The single celled green alga Chlamydomonas reinhardtii, while not an embryophyte itself, contains a green-pigmented chloroplast related to that of land plants, making it useful for study. The red alga Cyanidioschyzon merolæ has been used to study some basic chloroplast functions. Spinach, peas, soybeans, and Arabidopsis thaliana are commonly used to study plant cell biology too.

—Love, Kelvinsong talk 16:07, 30 June 2013 (UTC)

This is much better in my opinion. I'm ok with this. 512bits (talk) 09:51, 2 July 2013 (UTC)

I added it to the article with references—Love, Kelvinsong talk 14:00, 2 July 2013 (UTC)

Gene sequences

In paragraph 2 of Genetics, I don't like the way that having dealt with the gene sequences of rice and Brachypodium, a whole clutch more grasses turn up in the next sentence, with only a single dicot. Isn't anybody sequencing anything more interesting?. Plantsurfer (talk) 15:12, 30 June 2013 (UTC)

The first paragraph of genetics is little more than a badly-sequenced tutorial on generic genetics. There is nothing specific to plant genetics here, and therefore little that can justify being in this article. If there is nothing to say about plant genetics that is distinctive then it is not worth saying. Plantsurfer (talk) 15:12, 30 June 2013 (UTC)

This is only a general article on botany, not on plant genetics, so Arabidopsis thaliana and one grain would be fine, with a little more information about how these two relate to botany in general. --AfadsBad (talk) 15:45, 30 June 2013 (UTC)

Sorry, it is crass, and it has to go. Plantsurfer (talk) 16:08, 30 June 2013 (UTC)

I don't understand what you mean. What is crass and has to go where? --AfadsBad (talk) 16:26, 30 June 2013 (UTC)

The first para of the genetics section which I deleted. I think we should work on a better replacement for it, which specifies what is special and different about plant genetics. I will think about that (see below for ruminations so far), but meanwhile, if you have any good ideas . . . Plantsurfer (talk) 16:40, 30 June 2013 (UTC)

Yes, I thanked you for removing it, so I am obviously not disagreeing with its removal. --AfadsBad (talk) 17:23, 30 June 2013 (UTC)

We must be able to make a better statement of plant genetics than this.

First we need to acknowledge the article of that name with a link. I am not making any endorsement of its content, but there are points there that we should summarise in Botany#Genetics e.g.

What is distinctive about plant genetics?:

1) the genes for the outer membrane of the chloroplast are encoded in plant nuclear DNA, while the rest of the chloroplast has its own genome, in the same way as in mitochondria

2) the chloroplast genome is passed to offspring via the pollen in gymnosperms, but via the maternal line in angiosperms. Similar generalization (with exceptions) applies to mitochondrial inheritance. see H.L.Mogensen (1996) The hows and whys of cytoplasmic inheritance in seed plants. Amer. J. Bot. 83 (3) 383-404.

3) polyploidy is common in the plant kingdom. why??? its function is....??? Speciation by ploidy (rare in animals)

4) How are plastids inherited by daughter cells during cell division?

5) Cytoplasmic male sterility

6) weaker species boundaries, breeding barriers, speciation by crossing

7) tunica corpus, chimeras, clones, plant propagation

Then, Given the importance of transgenics/GM both to fundamental plant science research and to practical applications of plant breeding there needs to be a statement on the subject here. Plantsurfer (talk) 16:52, 30 June 2013 (UTC)

[edit conflict] For the first, that sounds very suspicious—it varies depending on the species, but the chloroplast DNA rarely codes for more than a couple hundred things, and a lot of the stuff inside the chloroplast also comes from the nucleus/cytosol (that's the point of the Tic-toc complexes). I've heard of at least one chloroplast DNA-encoded protein on the inner chloroplast membrane, nobody really knows for sure what goes on at the outer membrane. (This source says the proteins are from the nucleus [5]) Also, the outer chloroplast membrane is now known to be cyanobacterial, not eukaryotic. Mitochondria are not my forte, in animals their genomes are even smaller than the chloroplast DNAs—it's mainly a few tRNAs and redox proteins if I remember right. Though in plants, the mitochondrial DNA is just as big or bigger than the chloroplast DNA, so maybe that should be mentioned. Someone should probably look into this.

For the second point, it should be noted that a few angiosperms inherit chloroplasts paternally too. (See Chloroplast#Chloroplast inheritance)

Polyploidy as a speciation mechanism? I have a bio textbook that devotes a whole section to it.

That would be good as a source then. Is there a succinct summary statement that can be extracted from it?? Plantsurfer (talk) 16:52, 30 June 2013 (UTC)

Plastid inheritance in mitosis—In algae it's tightly regulated, I think in plants its just random and depends on where a given chloroplast is in the cell. Should be mentioned that all chloroplasts can be traced back to proplastids in the meristems.—Love, Kelvinsong talk 16:41, 30 June 2013 (UTC)

Draft Genetics paras

Species boundaries in plants can be weaker than in animals, and cross species hybrids are often possible. A familiar example is peppermint, Mentha × piperita, a sterile hybrid between Mentha aquatica and spearmint, Mentha spicata. The many cultivated varieties of wheat result from multiple inter- and intra-specific crosses between wild species and their hybrids. In many angiosperms, self fertilization may be prevented by self-incompatibility mechanisms operating between the pollen and stigma, so that the pollen fails to germinate.

Unlike in higher animals, where parthenogenesis is rare, asexual reproduction may occur by several different mechanisms. The formation of stem tubers in potato is one example. Particularly in arctic and alpine habitats, where opportunities for fertilization of flowers are rare, plantlets or bulbs, develop instead of flowers, giving rise to clonal populations genetically identical to the parent. This is known as apomixis.

As in other eukaryotes, the inheritance of endosymbiotic organelles like mitochondria and chloroplasts is non-Mendelian. Chloroplasts are inherited through the male parent in gymnosperms but often through the female parent in flowering plants. Plantsurfer (talk) 21:40, 30 June 2013 (UTC)

Made some changes and comments—Love, Kelvinsong talk 23:43, 30 June 2013 (UTC)

And a few more. "Apomixis" needs spelling out, and it's a tricky term anyway. (User:Sminthopsis84 seems to understand this topic, judging by the edit history of the article, and may be able to help.) Peter coxhead (talk) 06:39, 1 July 2013 (UTC)

Thanks for your contribs. I have made some more changes above, and will contact User:Sminthopsis84 for advice on the apomixis statement. WP autocorrect keeps changing it back to apomixes - how can we train it? Plantsurfer (talk) 10:55, 1 July 2013 (UTC)

Now all we need probably is a succinct statement of the relevance of polyploidy to plant genetics and speciation. Plantsurfer (talk) 10:55, 1 July 2013 (UTC)

How about this, though it might be too long:

Plants often become autopolyploid, meaning they accidentally double their chromosome number in an event like a failure of cytokinesis. Most sexually reproducing organisms will be unable to produce viable offspring with other normal members of their species because their new chromosome number will be incompatible with them. However, since many plants can reproduce asexually, an autopolyploid individual can continue to reproduce, making a new species reproductively isolated from the parent species.

An allopolyploid plant can result from a hybridization event between two different species, which often results in sterile offspring with an odd number of chromosomes. It can still reproduce asexually, and a subsequent autopolyploidy event or hybridization events with the parent species can make the chromosome number even again, resulting in a new allopolyploid species.

—Love, Kelvinsong talk 13:11, 1 July 2013 (UTC)

Hi Kelvinsong - I have been drafting along similar lines, but is what you say actually correct? Polyploids have difficulty crossing with individuals of different ploidy levels, but tetraploid and hexaploid plants are often fertile, though reproductively isolated from each other (mismatch in n). Wheats are a case in point. Incidentally I think we should use something like this as an e.g.: "Durum wheat is a fertile tetraploid allopolyploid, while bread wheat is a fertile hexaploid. The commercial banana is an example of sterile, seedless triploid hybrid." I am not an expert on this topic unfortunately :-( Plantsurfer (talk) 14:42, 1 July 2013 (UTC)

It's complicated, isn't it. I see this line in the polyploid article under polyploid crops "The induction of polyploidy is a common technique to overcome the sterility of a hybrid species during plant breeding. For example, Triticale is the hybrid of wheat (Triticum turgidum) and rye (Secale cereale). It combines sought-after characteristics of the parents, but the initial hybrids are sterile. After polyploidization, the hybrid becomes fertile and can thus be further propagated to become triticale." Plantsurfer (talk) 14:42, 1 July 2013 (UTC)

Thanks Peter, it is true that I've worked fairly extensively on plant polyploidy and apomixis, and Plantsurfer, you are absolutely correct. Kelvinsong, it looks as if you may have picked up some of the work of G. Ledyard Stebbins who once responded to a question from a colleague of mine by saying that he concluded that he'd taken up the idea that autopolyploidy is common in angiosperms because he'd been rather overwhelmingly impressed by the colchicine experiments from the Albert Francis Blakeslee's lab, and could now see (this was at a conference) that there was a lot of evidence that autopolyploidy is not influential. Evidence has been accumulating in the last 50 years or so that autopolyploidy is rare in nature (and even more rarely viable), and that apomixis occurs in allopolyploids and is not (or almost never) an automatic byproduct of polyploidy, it requires alteration in several of the steps in reproduction (usually (1) bypass meiosis (2) bypass fertilization of the embryo (3) do something about the endosperm). New apomictic lineages seem to be usually the result of hybridization between a polyploid apomict and a sexual diploid. Sorry that I have to rush off right now, but I'll try to look in at intervals over the next few days. P.S.: "apomixes": no such English word, bugbear of apomixis researchers, ugh!. ]] (talk) 20:16, 1 July 2013 (UTC)

Thanks Sminthopsis84. I therefore propose the following text, which I hope indicates the basic facts while avoiding controversy. I hope you will correct any crassness.Plantsurfer (talk) 21:23, 1 July 2013 (UTC)

Most sexually reproducing organisms are diploid, with paired chromosomes, but doubling of their chromosome number may occur, resulting in polyploids, either due to errors in cytokinesis (autopolyploidy) or during normal processes of cellular differentiation (endopolyploidy), as in adult human heart muscle, where several ploidy levels are present.or like in human skeletal muscle cells, which can have multiple nuclei and therefore multiple sets of chromosomes. An allopolyploid plant may result from a hybridization event between two different species. Polyploid plants of both types can often reproduce normally, but may be unable to cross-breed successfully with the parent population if there is a mismatch in chromosome numbers, resulting in new species that are reproductively isolated from the parent species but live within the same geographical area. If sterile, plant polyploids can still reproduce asexually or by apomixis, forming clonal populations of identical individuals. Durum wheat is a fertile tetraploid allopolyploid, while bread wheat is a fertile hexaploid. The commercial banana is an example of a sterile, seedless triploid hybrid.

One of the textbooks I have (same authors but different from the other one—mainly it has more pictures) says that >80% of plant species come from polyploidy, should this be mentioned? The same textbook has a page about the wheats mentioned, except it has Emmer wheat as the tetraploid. Also can we just say that the heart cells have multiple nuclei, and therefore more DNA—"ploidy", while fun to say, is not a concept that's quickly understood. Plus the Cardiac muscle cell article says they only have one nucleus. A plant example would be best, but I can't think of one. Plantsurfer, hope you don't mind me putting the "draft box" around your text and adding a few links.—Love, Kelvinsong talk 23:19, 1 July 2013 (UTC)

Some suggested edits:

Most sexually reproducing organisms are diploid, with paired chromosomes, but doubling of their chromosome number may occur due to errors in cytokinesis. This can occur early in development to produce an autopolyploid or partly autopolyploid organism, or during normal processes of cellular differentiation to produce some cell types that are polyploid (endopolyploidy), or during gamete formation. An allopolyploid plant may result from a hybridization event between two different species. Both autopolyploid and allopolyploid plants can often reproduce normally, but may be unable to cross-breed successfully with the parent population because there is a mismatch in chromosome numbers. These plants that are reproductively isolated from the parent species but live within the same geographical area, may be sufficiently successful to form a new species. Some otherwise sterile plant polyploids can still reproduce vegetatively or by apomixis, forming clonal populations of identical individuals. Durum wheat is a fertile tetraploid allopolyploid, while bread wheat is a fertile hexaploid. The commercial banana is an example of a sterile, seedless triploid hybrid. Common dandelion is a triploid that produces viable seeds by apomixis.

Sminthopsis84 (talk) 07:46, 2 July 2013 (UTC)

Yes, that's good,I've added it in. Plantsurfer (talk) 09:09, 2 July 2013 (UTC)

Looks good.512bits (talk) 09:53, 2 July 2013 (UTC)

Transgenics, GM, Biotechnology

Should we make a brief statement about these topics, in view of the fact that students are abandoning botany courses in droves to pursue these topics in other departments (mainly biomedical where the job prospects are good and they pay in mazumas). Cynical, moi?? Plantsurfer (talk) 21:53, 1 July 2013 (UTC)

Cynical? No. Clearly, you've observed what's going on (we just lost someone from our lab to a job with real permanent prospects in a hospital). If someone can find suitable references, there is work on Arabidopsis that's been funded as important to fundamental cell biology (i.e., cancer research). A section on this sort of work doesn't necessarily, I think, have to be directed only towards agriculture. Sminthopsis84 (talk) 07:02, 2 July 2013 (UTC)

This will be good. I'll see what I can find.512bits (talk) 09:55, 2 July 2013 (UTC)

Excellent. If you can't find enough material, let me know. Sminthopsis84 (talk) 16:29, 2 July 2013 (UTC)

a very rough start below, feel free to add or change.....

Modern technology has greatly altered the study and nature of botany. It is no longer strictly the study of plants. Technologies such as Biochemistry, Biomedicine, Biotechnology, and transgenics that can improve functions in plants are altering the nature of the field. Fewer universities are offering botany as a major and are now integrating the material into other courses.

...512bits (talk) 21:42, 2 July 2013 (UTC)

Yes, this is a difficult thing to express. The last Botany undergraduate course in the UK, at Bristol Uni finishes up this month, so traditional Botany courses are gone. But aspects of plant science are still taught at undergraduate and postgraduate level, and there is great research activity and innovation still happening in places like Botanic Gardens and research institutes, and of course plant research is still of huge commercial interest (see Monsanto and Syngenta, for example). In the early 60s botanists still worked with whole plants much of the time, and knew at least a little about the key areas of activity in the subject and the people involved in research and teaching. But the subject has grown hugely and has became progressively more interdisciplinary so that all other areas of science have been brought to bear on the botany, so that 30 years later it had begun to fragment into sub-departments. Today, with new sub-disciplines such as molecular technology so dominant in biology and biomedical sciences, many people argue that the methods of study of all organisms are fundamentally the same and that the traditional boundaries between biological subjects are now irrelevant. All biologists use fundamentally the same research technologies. Plants are used to study aspects of human cancer, and most of those plants have been transformed with reporter genes derived from jellyfish. Many of the areas of study, e.g. of the structure of a single protein, are so complex and difficult that very specialized and costly equipment is required, and the research worker may not even work on the live plant but on the elaboration of a virtual model of the protein or even just a part of it in his computer. And if the protein is relevant to core metabolism, its structure may be virtually identical in plants and all other organisms. So the problem is not that Botany today is not about the study of plants, but that current understanding is that they are not totally different from animals or bugs, and that interdisciplinary research technologies have effectively made biology one huge playing field, so big that no single person can hope to take it all in anymore, resulting inevitably in fragmentation into new factions, often themselves cross-disciplinary, such as structural biology or evolutionary biology, or stem cell research. This is rant, you understand, not intended as draft. Plantsurfer (talk) 23:23, 2 July 2013 (UTC)

Since we're ranting, one consequence is that very soon there will be almost no academic botanists/plant scientists left who can identify plants. Let's hope that cheap DNA bar-coding comes soon! In about a week's time I'm going to the launch of a new Flora of the area of England where I live. Detailed knowledge of the distribution of plants is vital to the understanding of ecology, evolution, etc.; high quality Floras used to be at the foundation of the subject. University involvement in this Flora was limited to one senior (a.k.a. elderly) academic. University departments no longer regard the production of a Flora as a prestigious undertaking. Peter coxhead (talk) 08:13, 3 July 2013 (UTC)

Quite right, plant id doesn't get too much contact time here either, but students still want it, and other organizations like yours and mine provide their needs now. Universities don't much like practical applications of anything (agriculture, for example) unless they are suitable for spinning out a company. I look forward to seeing your Flora. We could learn from you how to go about collecting the data. Plantsurfer (talk) 10:06, 3 July 2013 (UTC)

Something to think about: http://aobblog.com/2013/07/seb2013-science-with-impact/ Plantsurfer (talk) 19:28, 3 July 2013 (UTC)

More perspective: http://www.botany.org/bsa/careers/car-cur.html Plantsurfer (talk) 09:03, 5 July 2013 (UTC)

So what to do with this topic? I think we're down to this and the making the lede good. 512bits (talk) 20:47, 4 July 2013 (UTC)

Stace, Clive (2010b). New Flora of the British Isles (3rd ed.). ....Hancock too

Who added this ref? It should probably have page numbers. 512bits (talk) 21:53, 4 July 2013 (UTC)

• • Stace fixed, need Hancock still. 512bits (talk) 23:27, 4 July 2013 (UTC)
• this one too: ^ Hancock, James F. (2004) Plant Evolution and the Origin of Crop Species. CABI Publishing. ISBN 0-85199-685-X. 512bits (talk) 22:12, 4 July 2013 (UTC)
  • this one is now fixed. Plantsurfer provided the page numbers. Thank you. 512bits (talk) 14:18, 5 July 2013 (UTC)

Refs and lede

• 1) two paragraphs in modern botany need refs. I'll see what I can find....got the first one, the one starting "20th century" still needs refs 512bits (talk) 15:00, 5 July 2013 (UTC)

maybe: http://www.plantcell.org/content/early/2012/02/21/tpc.111.093302.full.pdf+html D.W. Ehrhardt and W.B. Frommer (2012) New Technologies for 21st Century Plant Science. The Plant Cell February 2012, doi: http:/​/​dx.​doi.​org/​10.​1105/​tpc.​111.​093302 Plantsurfer (talk) 09:35, 6 July 2013 (UTC)

http://academia.edu/3314509/Under_One_Leaf._A_Historical_Perspective_on_the_UK_Plant_Science_Federation Plantsurfer (talk) 09:35, 6 July 2013 (UTC)

Look good. I added them.512bits (talk) 19:59, 6 July 2013 (UTC)

• 2) The lede needs the refs moved to the body if the topic is already covered. If not, that material needs added to the body with the ref moved there.

We're getting close! 512bits (talk) 15:00, 5 July 2013 (UTC)

Apart from 512bits comments on the lede, which I endorse, is the general opinion that the lede is adequate?? It better be, because this may be the only section people read! Plantsurfer (talk) 20:16, 6 July 2013 (UTC)

:-), the overall structure hangs together much better but we need to brainstorm what's there, to get rid of any remaining crassness, naivety and repetition, and subject the whole text to rigorous précis. All hands on deck! Plantsurfer (talk) 20:09, 6 July 2013 (UTC) aka Verbociraptor ;=)

Yes, I feel and agree it's time for good final review/précis now. If anyone feels more needs added, feel free to further improve. I'm no expert on what wikipedia wants but I feel the team has done a good job. And yes, I agree the lede is much better.512bits (talk) 02:00, 7 July 2013 (UTC)

Wrapup

1) First para in Plant Biochem needs refs. (I added two, ok?, can add more, 512bits (talk) 12:14, 7 July 2013 (UTC))

2) Did the clad thing we mention below get added?

3) We need to agree on British or American spelling. I've seen both.

4) The three refs still in the lede are specific to word etymology. We need to leave there. Or is there a way to put them in note or something? I'm not sure of the wikipedia rules on this.

512bits (talk) 02:00, 7 July 2013 (UTC)

Phylogenetics

I've expanded a brief mention of phylogenetics. I have some more refs to add but don't have time right now. I wonder if there should be a brief mention of cladograms, with a simple example? These are widespread in plant articles and botany textbooks. Peter coxhead (talk) 16:42, 6 July 2013 (UTC)

I had a similar thought. Cladistics should be mentioned here, if only with a link. Plantsurfer (talk) 17:54, 6 July 2013 (UTC)

I agree Peter, add it in when you have a chance. 512bits (talk) 19:28, 6 July 2013 (UTC)

Ok, will do. Feel free to revert/edit any additions. I've added an image (I like pictures!) which you may or may not like.

By the way, I don't know which of the Bibliography sublists Anderson (2001) should be in; please move if I haven't got it right. Peter coxhead (talk) 20:58, 6 July 2013 (UTC)

I love the cacti pics! 01:40, 7 July 2013 (UTC)

Excuse me if I missed it, did the clad thing that was mentioned get added? 512bits (talk)

No, I've added a paragraph now – a very heavily condensed summary of some 8 pages in Mauseth (2012). I started with Mauseth rather than another source to try to keep it relevant to plants. I'm not entirely happy with it; it's very condensed and I'm not sure what a reader who doesn't have some prior knowledge will make of it. It doesn't seem right to expand it much more in an article about botany; on the other hand, the "cladistic method" is fundamental to modern plant science, e.g. the APG stuff mentioned later. Again, feel free to amend.

Should there be an example cladogram too? We could condense the cactus one in Mauseth, perhaps putting in Euphorbiaceae. Peter coxhead (talk) 09:11, 7 July 2013 (UTC)

I think you did a good job. This is an overview article in a general encyclopedia vice an academic tome. A cladogram would be good, but I personally would like to keep the cacti double image in, so we may have to adjust the photo layout in that section. 512bits (talk) 11:25, 7 July 2013 (UTC)

Cladogram

I've tried three times to produce a cladogram for use in the article along with a short explanation, and not yet been happy with my attempts.

• The cladogram should ideally be related to something in the section.
• It needs to be simple, but yet of fairly substantial interest.

I tried:

• A simplified version of Mauseth's cactus cladogram, which fits with what's there before the cladogram will go. However, it seemed to need too much detail and too many different kinds of cacti to be simple enough for this article.
• An cladogram and explanation of why dicots are not now considered a natural group of angiosperms. This may still be the best, I now think. It relates to the next bit on the APG, but seemed a bit over-complex.
• An cladogram and explanation of why horsetails are now treated as ferns. I spent most time on this, and you can see the result here. However, I was mislead by the Fern article. If you follow up the two refs for the cladogram, which I should have done first, they don't support the version in the article. Recent sources still seem to leave the precise position of the horsetails unresolved. Also the groups of ferns are too obscure, I think, for this article.

Anyone have any other ideas? Peter coxhead (talk) 19:56, 10 July 2013 (UTC)

• • Perhaps use the style of the one you did on ferns, etc but use the info on dicots? 512bits (talk) 23:27, 10 July 2013 (UTC)

I'll have a look at it again when I get a chance. Peter coxhead (talk) 22:17, 11 July 2013 (UTC)

I've now added a very simple cladogram, which I think is probably enough for this article. Peter coxhead (talk) 09:32, 19 July 2013 (UTC)

Subdivisions of Botany

Could we please lose Cryptobotany from the list of subdivisions of botany? Plantsurfer (talk) 18:01, 7 July 2013 (UTC)

done 512bits (talk) 21:59, 7 July 2013 (UTC)

Plant anatomy and morphology

"A plant's body has two divisions—the root system and the shoot system, which contains leaves and stems." Erm . . how does this apply to mosses and liverworts?? It is a little angiospermist. Plantsurfer (talk) 23:23, 7 July 2013 (UTC)

"The root system and the shoot system cannot survive without each other—the usually nonphotosynthetic root system depends on the shoot system for food, and the usually photosynthetic shoot system depends on water and minerals from the root system." On the contrary, root cells are totipotent (see carrot), and can give rise to shoots, and vice versa. So the statement is not yet sufficiently clear and informative. Plantsurfer (talk) 23:28, 7 July 2013 (UTC)

This section still needs work to achieve accuracy and balance. Plantsurfer (talk) 23:36, 7 July 2013 (UTC)

Should probably forward this to Wikipedia:Wikiproject Countering systemic bias. The textbooks stress this root–shoot dichotomy so much I forgot about the mosses. Should definitely mention the adventitious roots and shoots stuff (on a side note, one of my neighbors recently cut down two trees to the stump after a fish-themed snowstorm disaster this winter, and there are now new shoots growing out of the old roots).

New draft?

With very few exceptions, the bodies of vascular plants including but not limited to ferns, gymnosperms, and angiosperms are divided into the root system (containing, obviously, roots) and the shoot system, which contains leaves and stems. Plants like mosses don't have true roots—nearly the entire plant is photosynthetic at some point (the sporophyte generation may become nonphotosynthetic at a certain stage of its life).

The root system and the shoot system are interdependent—the usually nonphotosynthetic root system depends on the shoot system for food, and the usually photosynthetic shoot system depends on water and minerals from the root system. Cells in each system are capable of creating cells of the other—these are called adventitious shoots or roots. Stolons are an example of shoots that can grow roots. In the event that one of the systems is lost, the other can often regrow it. In fact it is possible to grow an entire plant from a single leaf (as is the case with Saintpaulia) or even a single cell—which can dedifferentiate into a callus (a blob of unspecialized cells) that can grow into a new plant.

—Love, Kelvinsong talk 03:29, 8 July 2013 (UTC)

"Cell biology is the study of their structural and physiological properties, including responses to stimuli, cell division, development at the molecular and microscopic scales and their differentiation into tissues." Why is (was) this sentence in the plant anatomy section? It is relevant how?? Plantsurfer (talk) 23:55, 7 July 2013 (UTC)

That's all fine with me. 512bits (talk) 20:41, 8 July 2013 (UTC)

Finally got around to citing this and adding it to the article—Love, Kelvinsong talk 01:25, 12 July 2013 (UTC)

Progress

Are we nearly there yet? Plantsurfer (talk) 20:38, 8 July 2013 (UTC)

The Evolution section, paragraph 3 leads off with "Nonvascular land plants are embryophytes . . .". Embryophytes are defined in Scope and Importance, but that was a while back if you read at my rate and with my attention span :D Is it worth briefly reiterating the definition here?? Plantsurfer (talk) 20:26, 9 July 2013 (UTC)

I would think not. 512bits (talk) 00:27, 10 July 2013 (UTC)

Why not just remove "are embryophytes", it's like saying "red cars are automobiles.."—Love, Kelvinsong talk 00:57, 10 July 2013 (UTC)

Notable botanists still need to go away (the section). The people need to be included into the article. If they cannot be included in the article, then that probably means they are not notable enough for the article.--MarshalN20 | ^Talk 00:51, 10 July 2013 (UTC)

Support—I prefer the article to be more focused on methods and advances in the field rather than people.—Love, Kelvinsong talk 00:57, 10 July 2013 (UTC)

Support. A good number of those in the list are already in the body of the article. No need for duplication. And the remainder are either not sufficiently notable or could easily be replaced by others of equal or greater notability. Lists like this and the list of sub-disciplines are a sign of weakness in an article. They say "here's more stuff that we couldn't think how to organize into prose". Narrative text is to be preferred, or just leave them out. Plantsurfer (talk) 09:45, 10 July 2013 (UTC)

Support. And I agree with Plantsurfer's analysis -- make the article readable, put lists elsewhere. Also, there is a section at the bottom that has subdisciplines in a drop-down menu. --AfadsBad (talk) 13:02, 10 July 2013 (UTC)

Support. I've never liked the list of notable botanists, because it's OR unless it copies entries from one or more highly reliable secondary or tertiary sources. There's a case for some botanists that are not in the article being in an organized "See also" section, perhaps. I also agree that a drop-down menu of subdisciplines is better than a list. Peter coxhead (talk) 15:49, 10 July 2013 (UTC)

I think the case for that is diminished by the existence of List of botanists. Botany already links to List of botanists in the see also section, so job done imo. Plantsurfer (talk) 16:34, 10 July 2013 (UTC)

A "See also" section would include specific important botanists, while this list includes all botanists--potentially usefully or interesting, the former, while the latter is not useful at all. (Is there a bot that updates it?) --AfadsBad (talk) 16:44, 10 July 2013 (UTC)

I cut the notable botanists section per this agreement. 512bits (talk) 23:23, 10 July 2013 (UTC)

Botany subdisciplines template

These are the subdisciplines listed in the article that are not listed as such on the botany template:

• Agronomy

No. Separate applied science Plantsurfer (talk) 16:46, 10 July 2013 (UTC)

• (Algae) -- should be Phycology, see below

No. This is not a discipline, although it may be a topic. The discipline is Phycology Plantsurfer (talk) 16:46, 10 July 2013 (UTC)

• Arboriculture

No. Separate applied science Plantsurfer (talk) 16:46, 10 July 2013 (UTC)

• Bryology

Yes Plantsurfer (talk) 16:46, 10 July 2013 (UTC)

• Dendrology

No. Is this a discipline or merely a technique? Plantsurfer (talk) 16:46, 10 July 2013 (UTC)

• Economic botany

No. Separate applied science. Plantsurfer (talk) 16:46, 10 July 2013 (UTC)

I disagree, and this is the only one I can find a source for as a subdiscipline; that is why it is called "botany" with a qualifier though--it's a subdiscipline. But I agree with below that we should source these. --AfadsBad (talk) 22:35, 10 July 2013 (UTC)

• Forestry

No. Separate discipline. Plantsurfer (talk) 16:46, 10 July 2013 (UTC)

• Horticulture

No. Separate applied science Plantsurfer (talk) 16:46, 10 July 2013 (UTC)

• Lichenology

Yes Plantsurfer (talk) 16:46, 10 July 2013 (UTC)

• Mycology

Yes Plantsurfer (talk) 16:46, 10 July 2013 (UTC)

• Palynology

Yes Plantsurfer (talk) 16:46, 10 July 2013 (UTC)

• Phycology

Yes Plantsurfer (talk) 16:46, 10 July 2013 (UTC)

• Phytochemistry

Yes Plantsurfer (talk) 16:46, 10 July 2013 (UTC)

• Plant biochemistry

Yes Plantsurfer (talk) 16:46, 10 July 2013 (UTC)

• Plant genetics

Yes Plantsurfer (talk) 16:46, 10 July 2013 (UTC)

• Plant pathology

Yes Plantsurfer (talk) 16:46, 10 July 2013 (UTC)

• Plant systematics

Yes Plantsurfer (talk) 16:46, 10 July 2013 (UTC)

• Pomology

No. Separate applied science Plantsurfer (talk) 16:46, 10 July 2013 (UTC)

Currently on the template:

• Ethnobotany
• Paleobotany
• Plant anatomy
• Plant ecology
• Plant evolutionary developmental biology|Plant evo-devo
• Plant morphology
• Plant physiology

I was going to just edit the template, but maybe we could discuss what should be listed? --AfadsBad (talk) 16:29, 10 July 2013 (UTC)

• Comment I agree with Plantsurfer that we shouldn't treat agricultural or horticultural topics as subdisciplines of botany. My problem is then sourcing. Is there a sourced definition of a "subdiscipline" rather than, say, a "topic"? I can see that Paleobotany is a subdiscipline: it's often practised in a different university department (e.g. part of paleontology or geological sciences); it deals with issues outside "normal" botany, such as methods of fossilization or form classification; it has its own traditions, e.g. often seeming to use botanical names in a way closer to the zoological code; paleobotanists are poorly represented in IPNI* showing them to be a somewhat distinct group. But is plant morphology a "subdiscipline" or just a "topic" within botany? Peter coxhead (talk) 17:55, 10 July 2013 (UTC)
  * I had 14 added to IPNI myself and there are more lined up here. If you come across any authors not in IPNI, they do like to be told.
  • I agree with Peter and Plantsurfer. 512bits (talk) 23:29, 10 July 2013 (UTC)
    • I don't know if this helps, but it is at the very least some kind of source for considering specializations in Botany: http://www.botany.org/resources/botany.php#Specialization Plantsurfer (talk) 23:36, 10 July 2013 (UTC)
      • A possible solution would be to create the article Subdivisions in Botany (or Specializations in Botany) and link to it in Template:Botany. This would give us the scope to deal with a more comprehensive list of subdisciplines and specializations, give them as much explanation as needed and at the same time place them in organismal, applied etc. categories. The shortlist of subdisciplines listed in the template can then be seen as examples, rather than an OR selection. Plantsurfer (talk) 00:04, 11 July 2013 (UTC)
        • A search for Branches of Botany picks up loads of stuff from within WP - micropaleaoethnobotany (no, not really but almost!) - the subject really is very broad. I think this would make a good title. Plantsurfer (talk) 00:22, 11 July 2013 (UTC)

I'm ok with cutting what you proposed if that helps. 512bits (talk) 21:09, 13 July 2013 (UTC)

Botany, etymology

I feel I have to challenge, once again, the etymology of Botany as stated in the article.

The article states ".... and that from βόσκειν boskein, "to feed or to graze" " attributing the source to Online Etymology Dictionary. Firstly, the words "and that from" have no subject in the preceding part of the sentence, so the meaning is obscure. Secondly, the Online etymological dictionary does not refer to boskein as a source for the words botany or botanic. Here are the relevant entries in the dictionary:

"botany (n.) 1690s, from botanic. The -y is from astronomy, etc. Botany Bay so called by Capt. Cook on account of the great variety of plants found there.

botanic (adj.) 1650s, from French botanique (17c.) or directly from Medieval Latin botanicus, from Greek botanikos "of herbs," from botane "a plant, grass, pasture, fodder." The Greek words seems to have more to do with pasturage than plants; cf. related botamia "pastures, meadows," boter "herdsman," boton "grazing beast." " Plantsurfer (talk) 22:10, 10 July 2013 (UTC)

This agrees with the Oxford Concise Dictionary of English Etymology (1993). The chain is firmly Greek βοτάνη to βοτανικός to Latin botanicus then either directly or via the French botanique to English "botanic", with "botany" a back-construction. However, Wiktionary gives the derivation of βοτάνη as from βόσκω, which is the modern Greek equivalent of βόσκειν (the latter is the ancient infinitive; modern Greek doesn't have an infinitive and the first person ending in -ω is used in dictionaries instead). Several online New Testament Greek concordances (easily found by a Google search) give the same origin of βοτάνη. The suggestion is that originally βοτάνη mean something like "a thing suitable for a grazing animal to eat". I've re-written the lead a bit. Peter coxhead (talk) 23:00, 10 July 2013 (UTC)

I agree with Peter and his changes on this one. Good job. 512bits (talk) 23:32, 10 July 2013 (UTC)

like Plantsurfer (talk) 23:40, 10 July 2013 (UTC)

Conclusion from etymology?

The text says Botany began in prehistory as herbalism with early human efforts to identify—and later cultivate—edible, medicinal and poisonous plants ... Perhaps the etymology suggests that it began with efforts to identify suitable fodder for domesticated grazing animals? (This is OR, of course, unless a source can be found for this view.) Peter coxhead (talk) 08:57, 11 July 2013 (UTC)

Domestication of animals came rather late in the day though. Humans were hunter-gatherers and herbalists first, farmers much later, only comparatively recently. Some Amazonian tribes (for example) still live this way, hunting, fishing, growing some crops, but with deep knowledge of wild plant species and their uses for food (figs) in medicine, hunting (curare) for recreation as stimulants and in religious ceremonies as mind-altering drugs. I don't think it would be too hard to find a source to substantiate this view, but this early herbalism predates recorded history. The Greek fodder-centric view was very avant-garde, and comes from a culture that had settled into agriculturalism and recorded their history. Plantsurfer (talk) 10:41, 11 July 2013 (UTC)

Yes, but did ithe word botany originate with the prehistoric herbalism? We're talking about the word itself here, not the early science. 512bits (talk) 02:37, 13 July 2013 (UTC)

We talk about both of these things in the lede in separate sentences, and the herbalism origin appears again in Early Botany. I personally don't see any confusion or conflict between them. I don't see the need to labour the point about efforts to identify suitable fodder for domesticated grazing animals. Plantsurfer (talk) 10:12, 13 July 2013 (UTC)

It's only a few extra words. I happen to like the change the change Peter made. 512bits (talk) 11:27, 13 July 2013 (UTC)

Font for "grc-Latn" text

I was getting a strange appearance for text marked as in "grc-Latn", e.g. {{lang|grc-Latn|botane}} which renders as "botane"; basically the text was very condensed. I found the reason at Template talk:Lang#Screwing up formatting. Marking text as "grc-Latn" puts it in the font which is specified in your browser for use in displaying Greek characters. But this isn't right: it's a Latin alphabet version of Greek and should be displayed in the normal font for text. I can fix it by changing the font used for Greek characters to the one I use for normal text, but this font not as good for Greek, so I shouldn't have to do this.

I conclude that {{lang|grc-Latn|...}} shouldn't be used until this problem is fixed, so I'm going to remove it. Peter coxhead (talk) 08:34, 11 July 2013 (UTC)

Plant responses to internal and external signals (Oh great, more botany stuff???)

Well, in my biology textbook there's an entire section dedicated to plant responses to internal and external signals, yet I don't see much mention of that in this article. Shouldn't there be some stuff on studying plant hormones and light responses?—Love, Kelvinsong talk 01:30, 12 July 2013 (UTC)

I would support this, it is important 20th century understanding, provided the statement can be kept brief. This should be an article summarizing what the scope of botany is, not a comprehensive account of its information content. Plantsurfer (talk) 09:00, 12 July 2013 (UTC)

I think this would be good too. What I have onhand doesn't have such a section. I do see some things on the 'net though. Could you add this bit? 512bits (talk) 11:29, 13 July 2013 (UTC)

I'm willing to have a go at roughing it out, although I am no expert in this area. I am a bit daunted at the huge information content. Plantsurfer (talk) 21:28, 13 July 2013 (UTC)

Here's some basic topic points you should hit to help you out—

• Auxin
• Cytokinins
• Other plant hormones (giberellins, ethylene, abscisic acid, etc)
• Phototropism
• Gravitropism
• Other tropisms (touch, etc)
• Deëtiolation
• Long night/short night plants

—Love, Kelvinsong talk 21:42, 13 July 2013 (UTC)

aaarrgghhh! :-) Plantsurfer (talk) 22:14, 13 July 2013 (UTC)

I think going into more than a paragraph would be too much detail for a general/overview article. 512bits (talk) 22:51, 14 July 2013 (UTC)

Preliminary draft hormones

Here is a preliminary draft. I don't pretend it is complete or polished, but some of you might like to add your bit or hack it. Plantsurfer (talk) 13:29, 14 July 2013 (UTC)

Draft

1. A plant shoot (e.g. maize coleoptile) with the sun positioned directly overhead. Auxin (the pink dots) is evenly distributed within the shoot tip. 2. The sun is positioned at an angle to the shoot, causing auxin to move to the opposite side and stimulate the cells there to elongate. 3,4. This results in heliotropism, the shoot curving to follow the sun.

Plants are not passive, but respond to external signals such as light, touch, and injury by moving or growing towards or away from the stimulus, as appropriate. Tangible evidence of touch sensitivity is almost instantaneous collapse of leaflets of Mimosa pudica, the insect traps of Venus flytrap and bladderworts and the pollinia of orchids.

The hypothesis that plant growth and development is coordinated by Plant Hormones or plant growth regulators first emerged in the late 19th century. Darwin experimented on the movements of plant shoots and roots towards light and gravity, and concluded "It is hardly an exaggeration to say that the tip of the radicle . . acts like the brain of one of the lower animals . . directing the several movements". About the same time, the role of Auxins (from the Greek auxein, to grow) in control of plant growth was first outlined by the Dutch scientist Frits Went. The first known auxin, Indole-3-acetic acid, which promotes cell growth, was only isolated from plants about 50 years later. This compound mediates the tropic responses of shoots and roots towards light and gravity.

Cytokinins are a class of plant hormones named for their control of cell division or cytokinesis. The natural cytokinin zeatin was discovered in corn, Zea mays, and is a derivative of the purine adenine. Zeatin is produced in roots and transported to shoots in the xylem where it promotes cell division, bud development, and the greening of chloroplasts. The gibberelins, such as Gibberelic acid are diterpenes synthesized from acetyl CoA via the mevalonic acid pathway. They are involved in the promotion of germination and dormancy-breaking in seeds, in regulation of plant height by controlling stem elongation and the control of flowering. Abscisic acid (ABA), which occurs in all land plants except liverworts, and is synthesized from carotenoids in the chloroplasts and other plastids. It inhibits cell division, promotes seed maturation, and dormancy, and promotes stomatal closure. It was so named because it was originally thought to control abscission. Ethylene is a gaseous hormone that is produced in all higher plant tissues from methionine. It is now known to be the hormone that stimulates or regulates fruit ripening and abscission, and it or the synthetic growth regulator Ethephon which is rapidly metablized to produce ethylene, are used on industrial scale to promote ripening of cotton, pineapples and other crops.

Venus's fly trap, Dionaea muscipula, showing the touch-sensitive insect trap in action

Another class of phytohormones is the jasmonates, first isolated from the oil of Jasminum grandiflorum which regulates wound responses in plants by unblocking the expression of genes required in the systemic acquired resistance response to pathogen attack.

Discussion

Best wishes, Plantsurfer (talk) 13:29, 14 July 2013 (UTC)

Would someone like to have a crack at editing a sentence or two on Phytochrome, red and far-red response, etc?? I don't know enough about it. Plantsurfer (talk) 18:20, 14 July 2013 (UTC)

This is a botany article, a sentence on auxins and cytokinins with a sentence on phytochromes without red and far red response should suffice. --18:59, 14 July 2013 (UTC)

So do you think the material here is already more detail than necessary? What do others think?Plantsurfer (talk) 19:13, 14 July 2013 (UTC)

Yes, way over detailed in a way that blocks the basic understanding of why plant hormones are so important to botany. One sentence or two on each, what it is, how and why botanists study it, you know, why we mentioned these hormones. --AfadsBad (talk) 00:54, 15 July 2013 (UTC)

This video doesn't appear to work, and is too large. Are there fixes for this?

This video works fine for me. I use FireFox. Above I said one para is enough, but I really like the video and the image above, so I can be persuaded for enough text to allow for placement of both files ;-) We'd need to cut down the space the venus fly trap takes as this is too overwhelming. 512bits (talk) 22:57, 14 July 2013 (UTC)

OK, so would you like to make the change to the article, since I can't properly see what I'm doing?? Plantsurfer (talk) 23:27, 14 July 2013 (UTC)

Sure. Where would you like it to appear? If it's in a separate section, what section name? Just "Hormones"? 512bits (talk) 23:28, 14 July 2013 (UTC)

I suggest create a subsection in Plant physiology called "Plant hormones". There is also a sentence in the second para of in Modern Botany that reads "The discovery and identification of the plant hormone auxin by Kenneth V. Thimann in 1948 enabled regulation of plant growth by externally-applied chemicals. Frederick Campion Steward pioneered techniques of micropropagation and plant tissue culture controlled by plant hormones.[32]" I suggest leave the wording of that as is, but link "plant hormones" to the new section, i.e. plant hormones. Plantsurfer (talk) 23:39, 14 July 2013 (UTC)

Works for me! On it. I hope the photos don't cause a display mess. 512bits (talk) 23:46, 14 July 2013 (UTC)

The flytrap photo sticks down into the next section. We need to expand the section, or maybe if we trim the caption to the sun photo it'll do the trick. This is how it appears on my computer at any rate. 512bits (talk) 23:54, 14 July 2013 (UTC)

Looks pretty good to me. We haven't added a bit about phytochrome yet, so maybe that will straighten things up a bit, but anyway I think it looks great. I still can't figure out why I can't make the video work on my machine - it looked fine when I ran it from WM Commons. Plantsurfer (talk) 00:03, 15 July 2013 (UTC)

Done with the refs now. We still need to fix the flytrap layout somehow. Someone may still be planning to add a cladogram too. I added a bit about phytochromes but it needs expanded.512bits (talk) 19:52, 15 July 2013 (UTC)

I wonder if I might add a couple of paragraphs about pivotal moments in 20th century Botany.??

The finding in 1939 that plant callus could be maintained in culture containing IAA, followed by the observation in 1947 that it could be induced to form roots and shoots were key steps in the development of plant biotechnology.

Agrobacterium tumefaciens, a soil rhizosphere bacterium, can attach to plant cells and infect them with a tumor-inducing Ti plasmid by horizontal gene transfer, causing a callus infection called crown gall disease. Schell and Montagu (1977) hypothesized that the Ti plasmid could be a natural vector for introducing the Nif gene responsible for nitrogen fixation in the root nodules of legumes and other plant species. Today, genetic modification of the Ti plasmid is one of the main techniques for introduction of transgenes to plants and the creation of genetically modified crops.

Fine with me. 512bits (talk) 02:11, 17 July 2013 (UTC)

DOI error

I can't figure out what is wrong with the DOI in this ref. When you click on the DOI link in the Plant Cell journal article, it works, but in our wiki botany article it doesn't work. Can someone help? Here it is ... "Sussex, I. (2008). "The Scientific Roots of Modern Plant Biotechnology" (PDF). The Plant Cell 20. doi:​​​10.​1105/​tpc.​108.​058735Check |doi= value (help)". thanks 512bits (talk) 23:03, 17 July 2013 (UTC)

It's a bunch of zero-width spaces in ASPB journal dois—something I discovered a few weeks ago. I wrote to them about it but they never responded. Use Copy Link Location.—Love, Kelvinsong talk 23:08, 17 July 2013 (UTC)

How do I do that?512bits (talk) 23:18, 17 July 2013 (UTC)

I think if you put it into google, the spell-check will clean up the doi for you.—Love, Kelvinsong talk 01:41, 18 July 2013 (UTC)

Sorry, I still can't get this to work. 512bits (talk) 02:06, 18 July 2013 (UTC)

Try this: 10.1105/tpc.108.058735 —Love, Kelvinsong talk 02:19, 18 July 2013 (UTC)

Nope, still not working. See edit of 18:28. 512bits (talk) 22:30, 18 July 2013 (UTC)

Some citation bot fixed this but also made a bunch of bad edits.512bits (talk) 00:12, 20 July 2013 (UTC)

Tidying

Systematics section - the word Systematics is used in the title, but the section leads off with Scientific classification in botany. Systematics is not defined, and the word is not used again as a noun, although a later sentence uses it as a gerund "The cladistic method takes a systematic approach to characters". Could someone more taxonomically (sensu lato) literate than I please have a look at whether Systematics is the appropriate title of the section, and if so give it a brief definition. Plantsurfer (talk) 12:35, 18 July 2013 (UTC)

I still find all these terms – systematics, systematic botany, taxonomy – very confusing, and the more attempts I make to find definitions, the less sure I am what any of them mean as they are actually used by botanists. For example, it's said that taxonomy is a wider term than systematics, yet the journal of the American Society of Plant Taxonomists is called "Systematic Botany", implying that taxonomy and systematic botany are the same – why have a journal which doesn't cover the whole of your area? User:Sminthopsis84 has a self-description as a "systematic botanist" on his/her user page, so perhaps s/he can help! Peter coxhead (talk) 18:30, 18 July 2013 (UTC)

Sorry to be part of the frustration here! The international association similarly states that their aim is to promote systematics, though they call themselves taxonomists. When I next make it to the library, I'll try looking in Julian Huxley's The New Systematics to see if there is a definition there. As I've mentioned previously in discussion about this, I was taught that systematics is the methods of investigating relationships and evolution, and taxonomy is the result that one aims for (a classification), so I see systematics as not about matters such as nomenclature, but there are definitions that have been incorporated into the relevant pages that say otherwise. More anon, if sanity holds long enough under the strain of reading this material. Sminthopsis84 (talk) 20:14, 18 July 2013 (UTC)

God forbid I should cause you stress with these questions!:-) Plantsurfer (talk) 20:29, 18 July 2013 (UTC)

Thank the deity for that proscription! ;-) Sminthopsis84 (talk) 20:09, 19 July 2013 (UTC)

Well, I wouldn't go that far - it was issued by proxy! ;-)Plantsurfer (talk) 20:38, 19 July 2013 (UTC)

To add to the evidence re the international association, they say "TAXON is the bi-monthly journal of the International Association for Plant Taxonomy and is devoted to systematic and evolutionary biology". Now if Taxon isn't about taxonomy, what is?! Is "taxonomy" becoming a term to avoid, like "botany"? Instead of "botanical taxonomy" (so last century) we have "plant systematics". Peter coxhead (talk) 22:11, 18 July 2013 (UTC)

There has been a reluctance to use the word taxonomy, as Quentin Wheeler wrote in his 2008 book The New Taxonomy (note the title) ""When Julian Huxley edited The New Sytematics in 1940, he may not have appreciated fully the extent to which it would provide the battle cry for those who would dilute, detract from and eventually decimate taxonomy." I, for one, would argue that avoiding a word is not a good approach, though. Sminthopsis84 (talk) 20:09, 19 July 2013 (UTC)

I'm not arguing with that, just wonder whether the article should state that case, and whether the variety of alternative words/phrases used in the article makes it more complicated for the reader to understand. Plantsurfer (talk) 22:26, 18 July 2013 (UTC)

The more I learn, the more I realize how little I know. I think we if we try to explain all this we'll make matters worse. Let's go with one term, whatever we feel is the most prevalent today, and stick with it. 512bits (talk) 22:33, 18 July 2013 (UTC)

I hadn't read the essay here, which does seem to confirm the view that the most common usage now is systematics = taxonomy, regardless of what the historical or logical uses are. So I think the section heading is right, and we should give a short definition, something along the lines of the relationships of organisms and their evolutionary history. Peter coxhead (talk) 08:13, 19 July 2013 (UTC)

I just reread it too, like it very much, and have added a citation to it in Taxonomy (biology). It is a blog, but one of those extremely scholarly blogs. I've searched for a published version of it, but suspect that no such thing has appeared yet. Sminthopsis84 (talk) 20:09, 19 July 2013 (UTC)

I've changed the section title to "Systematic botany" – this seems to me actually less contested as to its definition than "systematics" alone. I've added a source and slightly copy-edited the opening to explain that systematic botany is related to classification, taxonomy and phylogeny – which are the actual subjects of the section. Does this work? Peter coxhead (talk) 08:54, 19 July 2013 (UTC)

Yes it does, that is much better. Plantsurfer (talk) 09:50, 19 July 2013 (UTC)

Yes, I agree that it's better now. Sminthopsis84 (talk) 20:09, 19 July 2013 (UTC)

Bibliography

I am the one that broke the bibliography into different sections. But it appears this is rather unusual for wikipedia. Shall I merge it all into one section like I see on other articles? 512bits (talk) 22:35, 18 July 2013 (UTC)

I would prefer that. I find the current method a bit complicated. But then I am a dinosaur.Plantsurfer (talk) 23:21, 18 July 2013 (UTC)

At first I thought the division was useful for what is a top-level overview article, but then I added a few sources and realized that the sections overlap. So I think that it may be best to have a single section. On the other hand it would be useful to readers to be able to flag up some further reading at the approximate level of Wikipedia, though I'm not quite sure how best to do this. Peter coxhead (talk) 07:56, 19 July 2013 (UTC)

I'm sure there are some refs that were in use and are not now in use due to all the editing that has occurred. Is there an easy way to tell that? I'll see if I can figure some out. 512bits (talk) 00:11, 20 July 2013 (UTC)

Evolution

This sentence in Evolution: "The ancestors of angiosperms are a sister clade to the gymnosperms." Ambiguous. Discuss. Are not angiosperms a sister clade to gymnosperms? Are not the ancestors of angiosperms part of the same clade? Plantsurfer (talk) 22:37, 19 July 2013 (UTC)

On the Hybrid Origin of the Angiosperms. G. Ledyard Stebbins Evolution Vol. 12, No. 2 (Jun., 1958), pp. 267-270. Does anyone still hold to that view or one like it? I've no idea. Perhaps that wasn't the point though. I don't see how "ambiguous" could apply here.Sminthopsis84 (talk) 22:33, 20 July 2013 (UTC)

I don't have access to the source given, but on the basis of other sources, I think the following may be meant. (1) "Angiosperms" are defined by apomorphies. (2) When extinct plants are included, the sister clade of gymnosperms contains plants which are not, by this definition, angiosperms. (3) Hence the source of the statement doesn't want to say that angiosperms are sister to gymnosperms.

However, it should be ok (on the basis of most current phylogenies) to say that living (extant) angiosperms and gymnosperms are sister clades. However, there are signicant sources with cladograms showing non-monophyletic gymnosperms (the older morphological view), e.g. this 2013 paper. So we need to be careful in what we say here. Peter coxhead (talk) 06:49, 21 July 2013 (UTC)

Plant Physiology

"The energy of sunlight, captured by photosynthesis and released by cellular respiration, is the basis of all life." Not true. Marine communities in deep ocean can obtain all the energy requirements from sulphur reduction by . This sentence therefore needs subtle alteration. I would prefer to say "..basis of terrestrial life" (Botany being mainly concerned with Land Plants) but this fails if terrestrial is read as life on earth. Any other views? Help. Plantsurfer (talk) 22:50, 19 July 2013 (UTC)

"the basis of almost all life" is true, but it would be nice to have a number, e.g. the relative energy capture by photosynthesis and chemosynthesis. I haven't been able to find one so far. Peter coxhead (talk) 06:56, 21 July 2013 (UTC)

"The sporophyte generation may become nonphotosynthetic at a certain stage of its life." Sourced, but terminally vague. What is it on about?? This sounds like a misunderstanding imo. Plantsurfer (talk) 23:21, 19 July 2013 (UTC)

From the context, this comment seems meant to apply to non-vascular plants, so it may be true but certainly isn't clear! Peter coxhead (talk) 07:08, 21 July 2013 (UTC)

I have copy-edited it now, so hope the new edits are clear. Plantsurfer (talk) 10:24, 21 July 2013 (UTC)

Yes, much better. Peter coxhead (talk) 10:55, 21 July 2013 (UTC)

ENGVAR of article

Currently the ENGVAR of the article is inconsistent, e.g. it has "colour" (BrE) and "fiber" (AmE). If it is to be taken through to FA status (which seems highly possible now), editors need to know the ENGVAR to ensure consistency.

• The article was created by an anonymous editor, and the first edits were by many different people, so a coherent style doesn't seem to have been established.
• MOS:RETAIN suggests looking at the first non-stub version, which is a bit complex, because the article went in and out of stub status, as material was taken out and moved to Plant. this is perhaps the first non-stub version under the current concept. It has "specialized", a marker of either AmE or Oxford BrE, but no good indicators like "color" vs. "colour".
• The first large addition, which firmly established it as a non-stub, was by User:Dullhunk, who isn't around now. S/he uses British spellings, both additions to the article (e.g. "utilise") and in his/her edit comments (e.g. "capitalisation"). At the end of his/her edits, there are only BrE spellings (the earlier "specialized" has disappeared).

So I think that by MOS:RETAIN, the article should probably be marked as in British English, and its style adjusted accordingly. Does anyone have any other views or objections? Peter coxhead (talk) 10:41, 21 July 2013 (UTC)

PS: the dashes are currently inconsistent between spaced en-dash (usual style in modern BrE) and unspaced em-dash (usual style in AmE). When the ENGVAR is agreed, these should be sorted accordingly. Peter coxhead (talk) 11:00, 21 July 2013 (UTC)

Support. Plantsurfer (talk) 11:06, 21 July 2013 (UTC)

I brought this up weeks ago but no one paid attention to it. If an article is tied to a locality, it's easy. But otherwise it's not so easy. MOS:Retain gives preference to the person with first mover advantage, which is not a method I like. An article being edited by a group mostly from one geographic area will tilt to that area. As to this Botany article, I'm not sure what to do except to say spelling, format, dashes, etc should be consistent.512bits (talk) 11:46, 21 July 2013 (UTC)

But to make them consistent, we have to pick an ENGVAR, and we do need strict consistency for FA. (I don't have any personal views on this article either way: I write new articles in Oxford BrE, but have taken AmE articles to GA.) All I can say is that following MOS:RETAIN by looking at the first major addition after stub status suggests BrE to me, and in this case there seems no other obvious way of making a decision. But I'm happy to go along with any other consensus. Peter coxhead (talk) 16:35, 21 July 2013 (UTC)

As no-one has objected, I'm going to add the relevant template here and copy-edit the article accordingly. Peter coxhead (talk) 16:00, 22 July 2013 (UTC)

As long as things are consistent.512bits (talk) 22:01, 22 July 2013 (UTC)

Sure. I'm not good at copy-editing on screen, so I'm currently working on a printed copy and will be back.

One thing needed for FA is alt text describing the images, if anyone has time to look at this. Peter coxhead (talk) 08:52, 23 July 2013 (UTC)

I think we need to take a good hard look at all the images and consider their notability, their connection with the accompanying text and their image quality. We all love Pinguicula, but I am not sure why it appears here as the article's first image. Crantz was a botanist, but the image says little about him or the subject, and lacks connection with the article. Hibiscus isn't the first plant one thinks of when considering the Scope and importance of Botany, so why is it representing this section? Rice to illustrate a section on human nutrition is good, but is this the best image available? A picture can only be worth a thousand words if it is the right picture in the right place. Plantsurfer (talk) 12:15, 23 July 2013 (UTC)

I agree. The images need to illustrate botany and things botanists do, rather than plants as such. Peter coxhead (talk) 14:28, 23 July 2013 (UTC)

Gallery of alternative images

• 
  might use this to replace Hibiscus. Its advantage is that it shows the product of the study of the plant, a prepared herbarium specimen.
• 
  Twinflower, Linnaea borealis, Caprifoliaceae, named after Carl Linnaeus
• 
  re Spice trade - Fruits of nutmeg showing the aril (mace)
• 
  This would be good to illustrate Plant Anatomy
• 
  Rhynia, a Devonian vascular plant fossil from Rhynie chert showing anatomical preservation
• 
  A botanist at work in the herbarium
• 
  A gymnosperm (cycad) cone showing the naked seeds
• 
  A botanical illustration showing the morphology of the rice plant
• 
  Cyperus papyrus culms were used by the ancient Egyptians to make papyrus for writing.
• 
  Carboniferous "Stanhope tree", Co. Durham UK and living angiosperm trees.
• 
  Flowers of Arabidopsis thaliana, Brassicaceae, model plant.
• 
  The Calvin cycle
• 
  Micropropagation of transgenic plants
• 
  Engraving of Cork cells from Hooke's Micrographia - the discovery is referred to in the article

You already made changes I would have made, but how about Arabidopsis thaliana as the lead photo? 512bits (talk) 12:18, 24 July 2013 (UTC)

Some more issues

Closed

• The article currently says: "In 1754 Carl von Linné (Carl Linnaeus) divided the plant Kingdom into 25 classes ... For the purposes of identification, Linnaeus's Systema Sexuale classified plants into 24 groups according to the number of their male sexual organs." Now 1754 is the 5th edition of Genera Plantarum and 25 is what it says at Carl Linnaeus#Genera Plantarum, but is this correct? What are the "25 classes" as opposed to the "24 groups"? Peter coxhead (talk) 15:01, 23 July 2013 (UTC)

Sminthopsis84 has corrected Carl Linnaeus#Genera Plantarum to 24, so I'll fix this article. Peter coxhead (talk) 20:28, 23 July 2013 (UTC)

 Done Peter coxhead (talk) 20:46, 23 July 2013 (UTC)

• "... and dispersal vectors distribute spores and seeds." If "dispersal vectors" is used here, it should be explained, but doesn't it just mean "things that distribute spores and seeds"? Peter coxhead (talk) 15:01, 23 July 2013 (UTC)

 Done – fixed by Plantsurfer. Peter coxhead (talk) 07:34, 24 July 2013 (UTC)

• "Plants are the fundamental base of nearly all terrestrial food chains". It's the word "terrestrial" which bothers me. Yes, if we define "plants" as embryophytes, then it's only true for land-based food chains. However, many textbooks don't make this distinction in this context, so it appears a slightly odd qualification. Maybe "Plants and other photosynthetic organisms are the fundamental base of nearly all food chains"? I'm not sure. Peter coxhead (talk) 16:39, 23 July 2013 (UTC)

I don't like the word fundamental much in this context or nearly all, so what about "Plants and other photosynthetic organisms are at the base of most food chains." Plantsurfer (talk) 17:42, 23 July 2013 (UTC)

Agreed.  Done Peter coxhead (talk) 20:46, 23 July 2013 (UTC)

Coleoptiles and phototropism

 Done

1. A maize coleoptile with the sun overhead. Auxin (pink) is evenly distributed in its tip. 2. With sun at an angle auxin moves to the opposite side and stimulates cell elongation there, 3,4. causing the shoot to follow the sun.

The picture used under Botany#Plant hormones depicts auxins migrating to the shaded side of the coleoptile causing cell elongation, but according to the textbook I have (), in most plants (not grass), it's actually a growth inhibitor that collects on the lit side of the stem that causes the curving. Plus, where in the image description page does it say the plant shown is corn?—Love, Kelvinsong talk 20:02, 23 July 2013 (UTC)

The author of the image just refers to it as a "normal plant" (whatever that might be) and doesn't say corn, but it surely is a coleoptile - just look at it. No self-respecting dicot shoot looks like that, and the classical experiments on auxin were done using maize coleoptiles. However, my caption is just a précis of the original image caption, and if you know that it is incorrect please feel free to edit it. Plantsurfer (talk) 21:01, 23 July 2013 (UTC)

The explanation and illustrations in Mauseth (2012, 5th ed., p. 351) are precisely as per the image caption. It specifically mentions an oat coleoptile. So I'll edit the article to source to this. Peter coxhead (talk) 15:35, 24 July 2013 (UTC)

Evolution

 Done The evolution section makes the unsourced claim that the earliest true seeds date from Middle Devonian. That is incorrect. True seeds by the article's own definition are integumented ovules, and the earliest stages of enclosure of pteridosperm pre-ovules with an integument can be seen in latest Devonian (Late Famennian) species such as Moresnetia and Elkinsia e.g. . The early Carboniferous species Stamnostoma (Long, A.G. (1960) Stamnostoma huttonense gen. et sp. nov. - pteridosperm seed and cupule from the Calciferous sandstone series of Berwickshire. Transactions of the Royal Society of Edinburgh 64, 201-215) is the first to have its ovule properly integumented. Plantsurfer (talk) 10:55, 25 July 2013 (UTC)

Number of botanical species

 Done According to lede, "Nowadays, botanists study about 400,000 species of living organisms." What is the source for that number, and what groups does it cover? According to Judd (see ref in article) the Tracheophytes number some 260,000 species of which about 248,000 are flowering plants. I think those numbers would make more sense to the "average reader" and at the same time illustrate the overwhelming dominance of Angiosperms. Plantsurfer (talk) 12:36, 28 July 2013 (UTC)

 Done

Groups? Possibly the most reliable current indicator of the range of organisms within the purview of Botany is the range covered by the International Botanical Congress and the ICN, which covers plants, algae, and fungi. No viruses there, although I acknowledge that plant viruses are studied by some botanists. So also are some bacteria (e.g. Rhizobium) and nematodes, but if there has to be a defined cut-off point, I suggest that the groups specified in the title of the ICN would be a good way to define it. Plantsurfer (talk) 13:08, 28 July 2013 (UTC)

So what are we doing on this point? 512bits (talk) 22:55, 9 August 2013 (UTC)

 Done

• "The ideas of natural selection as a mechanism for evolution required modifications to the Candollean system, which started the studies on evolutionary relationships and phylogenetic classifications of plants." What started "the studies"? Natural selection? Modifications to the Candollean system? I'm not sure what is meant here. Peter coxhead (talk) 15:01, 23 July 2013 (UTC)

It seems to be referring to natural selection. It does need a tweak.512bits (talk) 12:21, 24 July 2013 (UTC)

After reading this ref [6], I've convinced this clause refers to Candolle, I will tweak and add the ref. Let me know if any disagrees. 512bits (talk) 13:19, 26 July 2013 (UTC)

 Done

I'm sorry, but I don't think you have this right. Candolle's classification scheme was not intended to reflect evolution or phylogeny, but a concept of increasing complexity. Solely in that respect his classification was allied to Linnaeus's, but Candolle did not limit his scope to male organs, considering the broader picture. Bentham and Hooker built their classification along Candollean lines, again making no attempt to reflect evolution or phylogeny, but as the article you use as source states "the author's general ideas of morphological complexity". Darwin/Wallace changed all that. Your source article states "Classifications after Darwin and Wallace were predicated on an understanding of descent and evolution". That continues to be true. In fact descent, evolution, phylogeny are of overriding importance in modern botanical classification - as far as morphological complexity is concerned it is often misleading and, frequently, less is more. Plantsurfer (talk) 19:56, 26 July 2013 (UTC)

OK, then reword it. 512bits (talk) 22:37, 26 July 2013 (UTC)

OK, the bones of what I would want to say are in the above (clearly they will need cleaning up). Judd et al. (2002) Plant systematics a phylogenetic approach. on page 5 put the point about Darwin's influence like this: Publication of Charles Darwin's On the Origin of Species in 1859 stimulated the incorporation of general evolutionary relationships into classification, an ongoing process that has yet to be realized. This is therefore a good source for the idea that there has been a paradigm shift towards phylogenetic systematics following the assimilation of Darwin's theory of evolution by natural selection.

Open

• "Unlike in higher animals, where parthenogenesis is rare, asexual reproduction may occur by several different mechanisms." Parthenogenesis is defined in its article as "a form of asexual reproduction in which growth and development of embryos occur without fertilization", so it's not in contrast to stem tubers. The analogy with stem tubers would surely be something like budding in hydrozoans. Two different things seem to be run together here here: vegetative reproduction and non-vegetative apomixis. User:Sminthopsis84 has edited the apomixis article, so may be able to clarify this text; apomixis seems to be a very complex concept! Peter coxhead (talk) 15:01, 23 July 2013 (UTC)

• I'm not at all sure about the Evolution section. It seems to be trying to give an overview of the evolution of plants in a few paragraphs, which doesn't really work for me. Shouldn't it try to say something about the importance of evolution as an underpinning to botany and how botanists use and research evolutionary issues, rather than try to describe the evolutionary history of plants? Peter coxhead (talk) 15:01, 23 July 2013 (UTC)

(referring to Judd et al.) On page 3 they make the following remark: Systematics is not just descriptive (as were the classifications of de Candolle and B&H) but aims to discover (my bold) evolutionary relationships and real evolutionary entities that have resulted from the process of evolution. We also assume that evolutionary modifications within these lineages have happened and will continue to happen. I wonder Peter coxhead whether this is useful material for the Evolution section.??

The logical consequence of that understanding is that species names are merely snapshots in time, and that for some taxa it is clear that they have already changed almost before they have been fully described, but I don't know of suitable botanical taxa and sources to illustrate that. Plantsurfer (talk) 23:48, 26 July 2013 (UTC)

For the general issue that species are merely snapshots in time, Podani has written about this very clearly (e.g. Podani, J. (2010), "Taxonomy in Evolutionary Perspective : An essay on the relationships between taxonomy and evolutionary theory" (PDF), Synbiologia Hungarica, 6: 1–42) but not specifically in the context of botany. In the case of plants, there are two different issues which challenge the species concept: (1) change within a species over time, which also applies to animals (2) widespread hybridization between "species", which is rare in animals. Dactylorhiza in the UK, Ophrys everywhere are examples of the difficulty of defining species when hybrid swarms are frequent occurrences. I would like to work (2) into the article somewhere: along with polyploidy it represents an important difference between plants and animals. Peter coxhead (talk) 07:06, 28 July 2013 (UTC)

Support. I think those are very important points. Plantsurfer (talk) 10:03, 28 July 2013 (UTC)

Whatever you guys want to do in order to wrap up this improvement effort is fine with me. 512bits (talk) 21:15, 30 July 2013 (UTC)

I think my "to do" list is almost done (don't quote me), and I think we are at the stage of needing peer review to take this much further. Plantsurfer (talk) 21:21, 30 July 2013 (UTC)

I've got a couple of bits I want to change; I got rather distracted by another article which needed fixing and then another linked to that one – a perennial problem on Wikipedia! I'll try to get back to Botany in the next couple of days. (The alt tags in images need fixing before an FA review.) Peter coxhead (talk) 21:25, 30 July 2013 (UTC)

Peer review

Over on Peter's page he says he's ok with moving on and indicates he'll yet add a bit more. On my talk page Plantsurfer seems to be ready to move on to. Consequently, I have nominated this at peer review. I hope we get some some good, constructive reviews there. 512bits (talk) 01:18, 13 August 2013 (UTC)

Peer review results in. I'll start on them. Help appreciated. Link here: Wikipedia:Peer review/Botany/archive1 512bits (talk) 00:08, 19 August 2013 (UTC)

I have done several of these. Will continue later. 512bits (talk) 00:53, 19 August 2013 (UTC)

• Spice trade: I've removed this sentence which was queried in the review: "The spice trade was of great economic and political importance during the Middle Ages, driving world exploration." I think it could be expanded in the body of the article and then something put back in the lead, but I'm not quite sure what. However, if it's removed altogether, the image is wrong. Peter coxhead (talk) 14:33, 21 August 2013 (UTC)
  • OK. I can see the garden connection, but I think the spice trade is delving too far into economics. I don't the image is out of place. In fact, I've grown to like it. 512bits (talk) 23:44, 22 August 2013 (UTC)

• I just answered the last Peer Review item. I'm not sure how long we should let that run. I think the reviewer did a really good job. Some have mentioned getting this to "featured" status. 512bits (talk) 23:42, 22 August 2013 (UTC)

Self-pollination

Moving the sentence on self-pollination to the paragraph dealing with asexual reproduction makes little sense. Self-incompatibility is about sexual reproduction and the promotion of outcrossing in monoecious species such as brassicas. Perhaps what is missing here is a statement that many other species, and not just angiosperms, deal with this by being dioecious or dioicous. Plantsurfer (talk) 09:45, 13 August 2013 (UTC)

You're right, I moved it back. I'm not an expert on dioecy, etc, so you might want to write that part.—Love, Kelvinsong talk 16:58, 13 August 2013 (UTC)

Plant Biochemistry

Is there a plant biochemist in the house? We need a short paragraph on Plant Biochemistry that balances the existing Biochemistry section by outlining what the study of the biochemistry of primary metabolism is about. At present it is biased towards commercially useful secondary products. Any help here would be greatly appreciated. Plantsurfer (talk) 19:00, 22 August 2013 (UTC)

Could someone condense info from Plant physiology? 512bits (talk) 23:46, 22 August 2013 (UTC)

unfortunately, that article lacks sufficient depth of the kind we need :-( Plantsurfer (talk) 14:05, 23 August 2013 (UTC)

Curiously, Katherine Esau's Plant anatomy books are referred to but not cited. Plantsurfer (talk) 12:04, 23 August 2013 (UTC)

A basic plant biochemistry outline could be:

• +/– compartmentalization
• photosynthesis all the way to storage products
• nitrogen (and sulfur)
• membranes (and lipids)
• secondary metabolites moved into this section
• genes, reproduction and growth

Esau's book, although old, would be an excellent source for Wikipedia editors to use for plant physiology. That article's section on biochemistry should be removed, it is a jumble of words. -AfadsBad (talk)|

This draft is what I have in mind for the Biochemistry section, not an account of the general biochemistry that is common to all organisms, but a pointer to those aspects of biochemistry that are unique to or particularly characteristic of plants. More sources may still have to be added. Please help with this:

Aspects of plant biochemistry that are unique to plants include the synthesis of a number of unique polymers, the polysaccharide molecules cellulose, pectin and xyloglucan from which the plant cell wall is constructed, and the storage polysaccharides starch, (used in most land plants) and inulin used in the sunflower family Asteraceae. Cellulose is synthesized by an enzyme complex embedded in the cell membrane, while matrix polysaccharides are synthesized in the Golgi apparatus and exported into the cell wall. During growth, the cell wall must expand, and this is enabled by breaking and splicing the polysaccharide chains using specialized enzymes such as xyloglucan endotransglycosylase The phenylpropanoid polymer lignin is an innovation or synapomorphy of vascular land plants that is used to make the xylem cell walls more rigid and able to withstand the tension in the water column that results from water stress is also used in the thickened cell walls of xylem fibre cells. The monomers of lignin, coniferyl alcohol, paracoumaryl alcohol and sinapyl alcohol are synthesized from the amino acid phenylalanine. Sporopollenin, a chemically-resistant polymer found in the outer cell walls of spores and pollen of land plants, is responsible for the survival of early land plant spores and the pollen of seed plants in the fossil record. Lipid synthesis in plants occurs largely in the chloroplasts. The unique lipid polymer cutin that waterproofs the aerial surfaces of all land plants is a polyester made from omega hydroxy acids that are synthesized only in the epidermal cells from palmitic acid made by the chloroplasts of the mesophyll cells. Sucrose, the familiar table sugar and the sugar that is transported in the phloem of plants, is a disaccharide composed of a glucose and a fructose molecule. It is made only by plants and cyanobacteria by the enzyme Sucrose-phosphate synthase. The concentration of carbon dioxide in the atmosphere today is much lower than it was when plants emerged onto land during the Ordovician and Silurian periods. Many grasses, including maize and Sorghum, use the C₄ carbon fixation pathway for photosynthesis that avoids the losses resulting from photorespiration in the more common C₃ carbon fixation pathway. Crassulacean acid metabolism is a strategy used in the Crassulaceae and a number of other families including the pineapple family Bromeliaceae to accumulate carbon dioxide into malic acid at night, and use it to produce CO₂ with the stomata closed during the heat of the day, in order to reduce water loss. These biochemical strategies and the glycolate oxidase pathway are unique to land plants.

Plantsurfer (talk) 01:40, 24 August 2013 (UTC)

I think there is no organization in this, it is a shotgun of various end products of biochemical processes without order, moving from polymers to monomers, lipds, sugars, evolution of the atmosphere, the carbon cycle specifics, then close with a comment about the glycolate oxidase pathway? This is not keeping it at a general level of high importance, although the large amount of chemical text makes it hard to read. I am of the opinion that writing from a high level outline could create an appropriate introductory level section on biochemistry, but this shotgun approach will not. -AfadsBad (talk) 02:49, 24 August 2013 (UTC)

The part on cell plate formation seems correct though a bit irrelevant, and do we really need the enzyme names here? Agree with AfadsBad—in general this paragraph just looks like infodump. It's a really useful marble block, just needs to be chiseled down into that sculpture of words that FA requires. Also I am so stealing the part on cutin for the Chloroplast article. 😏—Love, Kelvinsong talk 18:37, 24 August 2013 (UTC)

Are we missing the point here gentlemen?? A large fraction of biochemistry is common to all organisms. Much of it is the same in plants and animals. Standard amino acid/protein chemistry, lipids, respiration etc. is all covered in Biochemistry. No way do we reiterate all that here. We have very little space. What we have to do, imho, is feature the aspects of biochemistry that are uniquely botanical, that represent the biochemical innovations that define plants. That's what the ""info dump"" above is about. Land plant evolution is characterized by a series of biochemical innovations, namely the capacity to synthesize polymers such as cellulose, sporopollenin, xyloglucan, cutin, lignin, (probably) in chronological order. This is not info dump, it outlines key steps of land plant evolution, without which none of us would be here. Glad you like the cutin bit Kelvinsong. Don't forget the epicuticular waxes. Plantsurfer (talk) 19:10, 24 August 2013 (UTC)

And photosynthesis has no place in a botany article, because the article should cover land plant evolutionary trends only? I am not following you, here. This is the botany article, and I think my high level outline is on target, and the jumbled infodump will get the same criticism in a FA review. Anyway, I think if you consult plant biochemistry books you might agree, although this seems like the request for assistance was a set-up. -AfadsBad (talk) 19:47, 24 August 2013 (UTC)

edit conflict

Well I get the feeling that it starts out that way and then loses its focus. A reader will probably come out of that paragraph thinking "wait what was I reading again?". I don't know if this is much better, but I took a shot at rewriting that paragraph (I think we should leave out or move the C₄ stuff if we're not going to mention photosynthesis)

Lots of aspects of biochemistry are common to all organisms, but some are unique to plants. Plants (and algae ^{(needs investigation regarding pectins and xyloglucans)}) are special in that they produce large quantities of certain polysaccharides like cellulose, pectin, and xyloglucan which are used in the process of building plant cell walls, as well as some storage polysaccharides like starch. When a plant's cells grow, they use special enzymes to break the crosslinks between the polymer chains in their cell walls allowing them to stretch. Plant cells also make polymers like lignin which go into the secondary cell walls of certain plant cell types to make them stronger—like in xylem tracheids and vessels where lignin helps prevent their cell walls from imploding when a plant sucks its water through them, and in other cells that provide support for a plant. Plants also have other tough polymers like sporopollenin (shared with some close relatives too) which protect their pollen grains and spores.

Plants and their close relatives have a unique organelle—the chloroplast—which plants have delegated many biochemical roles to besides photosynthesis. Unlike in animal cells, plant cells make all of their fatty acids in their chloroplasts. These fatty acids are used for many things like making the epidermal cutin that protects plants from drying out. In a plant's immune response, the chloroplast churns out a bunch of molecules that fight disease.

Sucrose, also known as common table sugar, can only be made by plants, cyanobacteria, and proteobacteria. Plants use the enzyme Sucrose-phosphate synthase to make it (some cyanobacteria employ different enzymes; little is known about how proteobacteria do it). Plants are thought to have inherited the ability from their chloroplasts (cyanobacterial endosymbionts). (Little is known about sucrose biosynthesis in algae, so we may want to leave this part out).

—Love, Kelvinsong talk 20:19, 24 August 2013 (UTC)

I agree that this should focus on the uniqueness of plant biochemistry. 512bits (talk) 21:02, 24 August 2013 (UTC)

"Plant biochemistry is the study of the chemical processes used by plants in their general or primary metabolism including the Calvin cycle and crassulacean acid metabolism used in photosynthesis,[67] and in the synthesis during growth of the specialised materials used in their construction, such as cellulose and lignin."

I don't understand this opening sentence's emphasis at all. This is way too detailed, and the emphasis is on certain non-primary aspects of parts of plant biochemistry. Does plant biochemistry exclude C3 and C4 photosynthesis, is it only about parts of photosynthesis? All of my plant biochemistry texts have the first half of the book about photosynthesis, not about CAM and the Calvin cycle. This section is completely misleading for the general reader, and I am looking for a template that says this. Still, I understand that my contribution/suggestion will be completely ignored, and that is okay, but the alternative results are not good for the reader. --AfadsBad (talk) 14:19, 26 August 2013 (UTC)

Chloroplast lipid synthesis

This may not even be relevant, but the part on chloroplasts making all the lipids (in that giant Biochemistry block that Plantsurfer put there last night, (nice work by the way!) ) seemed kinda suspicious. On very light investigation, I found this abstract that says the chloroplast and the endoplasmic reticulum work together to assemble the chloroplast's fatty acids into lipids. I think I also read somewhere else that the endoplasmic reticulum exports assembled lipids back to the chloroplast. Will look more into this later.—Love, Kelvinsong talk 16:22, 26 August 2013 (UTC)

The point about carotenoids and plants and algae is that those groups synthesize them. That is one of the characters that distinguishes the green algae from other algae that use phycobilins. If they are everywhere as you say (they are in egg yolk, for example and the retina of the human eye) it is because these heterotrophic organisms eat plants or green algae, not because they synthesize them. Plantsurfer (talk) 16:54, 27 August 2013 (UTC)

But the green algae aren't the only algae that make carotenoids. Rhodophytes, glaucophytes, etc. all have them too—see 1. In fact the carotenoid article says that fungi make them too.—Love, Kelvinsong talk 17:08, 27 August 2013 (UTC)

"Carotenoids comprise a large family of C40 polyenes and are synthesised by all photosynthetic organisms, aphids, some bacteria and fungi alike." Carotenoids in nature: insights from plants and beyond Christopher I. Cazzonelli Functional Plant Biology, 2011, 38, 833–847. --AfadsBad (talk) 17:13, 27 August 2013 (UTC)

Biochemistry - Medicine and materials

The last paragraph of Biochemistry introduces secondary metabolism. Are you happy with it where it is, or should it be moved into the Medicine and materials section? Plantsurfer (talk) 10:08, 28 August 2013 (UTC)

News to me that what plant biochemists do is study secondary metabolism. I will get my group off of all that oher stuff immediately. But, yes, I know, my comments are not part of the rewrite. Good in ways. -AfadsBad (talk) 13:33, 28 August 2013 (UTC)

Well of course you are welcome here, and since your expertise seems to be in this area your views should be duly considered, but you have tended to speak mainly in negatives, so it is difficult to know how to take account of them. I see secondary metabolism clearly as part of biochemistry - but not as the focus of it. That was the whole point of my recent additions and those of Kelvinsong, to respond to the reviewer's criticism that the article majored on secondary products. There surely cannot be any very clear demarcation between the study of primary metabolism and secondary metabolism. If, as you seem to argue, the chemistry of secondary metabolism should not be dealt with under the heading of Plant Biochemistry, how would you recommend the topic should be treated? If you see ways to make positive improvements in the article can you please discuss further this here? Plantsurfer (talk) 16:41, 28 August 2013 (UTC)

I have not said it should not be dealt with under biochemistry, in fact, the opposite, in my suggestion above, where I said it should be moved into this section, which everyone ignored. I think it would be easier to start at a high level with a broad discussion of biochemistry, but the consensus is some type of random fact farm. Seems time-wasting to me. Like my wasting my time researching and putting together my comment above. --AfadsBad (talk) 16:57, 28 August 2013 (UTC)

Also, by picking and choosing random facts, and then researching these out of individual articles, you are making errors of fact and of weight. --AfadsBad (talk) 16:58, 28 August 2013 (UTC)

Maintaining appropriate overall balance is difficult in an article as broad as this. I don't think it's at all fair to say that the consensus is "some type of random fact farm". The editors who have been working hard on this article started with what was there, which was much more of a set of random facts than it is now.

Often the way forward is to look at some standard textbook's coverage, and to map this in the article. Any suggestions? Peter coxhead (talk) 18:59, 28 August 2013 (UTC)

That seemed like a good idea, so I ran through the five biochemistry textbooks on my shelf and put together the outline I posted above. The same one where I suggested moving the secondary metabolites into the biochemistry section. The one that everyone is ignoring for some reason. That was and is still my suggestion. --AfadsBad (talk) 19:06, 28 August 2013 (UTC)

By the way, the books I used: Buchanan, Gruissem and Jones, 2002; Bowsher, Steer and Tobin, 2008; Lea and Leegood, 2nd, 1999; Gleason and Chollet, 2011 (online one, actually); and Heldt's 3rd, 2004. Mostly older, but newer outlines are similar, and all are plant biochemistry books. --AfadsBad (talk) 19:15, 28 August 2013 (UTC)

I can't claim to agree with your comments about random fact farm, but no matter. I admit that I had misunderstood what you were trying to say, and while I agree with some of it I don't agree with other bits. The main problem here is that we are trying to make a basic summary, not a full account of what is a very big subject. Whereas with some other sections of the article we have been able to rely on some reasonably adequate main articles to deal with the detail, here we are faced with the sad fact a) that there is no article on Plant Biochemistry and that b) such material as there exists is either stuck in a completely inadequate section in Plant Physiology (you think the same on this I gather), or is scattered about in multiple other articles. I personally object strongly to the whole topic of Plant Biochemistry being stuck in an article on Plant Physiology. It may work well enough in a textbook like Taiz & Zeiger, where there is enough space to write chapters in sufficient depth, but that is not how WP works. I think we should create the Plant Biochemistry article, and write it up properly. Perhaps your ideas could be put to best use doing that. If the idea has any peer support, I would be delighted to help in any way I possible can, although, as I have said previously, Biochemistry is not my specialist area. Best wishes, Plantsurfer (talk) 21:42, 28 August 2013 (UTC)

I still suggest that my outline, with just a few sentences, without specific "Chloroplasts and cyanobacteria contain the blue-green pigment chlorophyll a.[68] Chlorophyll a (as well as its plant and green algal-specific cousin chlorophyll b)[a] absorbs light in the blue-violet and orange/red parts of the spectrum while reflecting and transmitting the green light that we see as the characteristic colour of these organisms" is usable; but, I also see it will be entirely ignored. This sentence is not about botany, or even biochemistry in the summary sense; it is about some details of photosynthesis. Biochemistry, at the high level outline, is what botanists study to understand energy pathways, and photosynthesis is about molecules (a primary unit of biochemists) that convert light energy to chemical energy to make other molecules that the plant uses to create cell walls and control growth and reproduction; that's a basic summary, not chlorphyll a's absorption spectra!

The section on plant biochemistry in this article is picky, disorganized, and misses the main points, often due to undue emphasis on random points. Plant biochemistry is about the study of how plants make chemical molecules, ultimately from sunlight. What we have instead is this detailed section on specific molecules and details of those molecules without any overall context. You wind up not even wikilinking any of the fundamentals of biochemistry, because that information is lost in a too long sections full of randomly weighted details specific to subtopics. --AfadsBad (talk) 22:31, 28 August 2013 (UTC)

A suggested workable summary based on plant biochemistry textbooks

• [7]

I thought the original request for a possible paragraph length outline was reasonable. So, I responded with this post:

A basic plant biochemistry outline could be:

• +/– compartmentalization
• photosynthesis all the way to storage products
• nitrogen (and sulfur)
• membranes (and lipids)
• secondary metabolites moved into this section
• genes, reproduction and growth

It's been thoroughly ignored while a dense discussion of specific molecules and processes has been added to the botany article. This is a botany article, not a plant biochemistry article. The absorption spectra of chlorophyll a will not help general readers understand what plant biochemists study and how that is related to botany.

Botany is the study of plants, and part of the study of plants is, of course, how they grow and reproduce. They grow and reproduce by turning sunshine into molecules and transporting these molecules through the plant, as needed, inside and via specialized compartments within each plant cell (unlike a group of specialized cells organized into an organ in an animal). The process of converting sunlight into chemical energy is called photosynthesis. Plants require nitrogen and sulfur for specialized aspects of their biochemistry. They make cell membranes that create the individual compartments. The molecules that plants make are involved in their reproduction, in addition to growth. Plants create many useful secondary molecules that are used by humans or protect the plants from predation, among other things. --AfadsBad (talk) 22:43, 28 August 2013 (UTC)

There are two things left from the peer review: this biochem section and the fact that the article's technical level is inconsistent (which is from many different editors writing it) and too deep in places for an encyclopedia level article. I have to agree that this biochem section, while good and accurate, is too technical. It's also too long, it's the longest section in the article and hence has undue weight. The parts that get cut would serve well in the Biochemistry article. 512bits (talk) 23:19, 28 August 2013 (UTC)

FA nomination

(In response to User:Plantsurfer) I don't think this article is ready for FAC, but it's really close. I think the biggest problem, as 512bits said, is the prose. We need to talk about how many fancy words many of you have added to this article. When I read it, it's pretty clear that a bunch of British scientists (no offense) wrote most of it, in both the good and the bad way. Someone should be appointed to go through the article and smooth out the tone; if you think my writing is too casual that's fine, but let's make it consistent (and preferably less crusty).

To AfadsBad—yeah, that section definitely sounds like Moleculedump, but in my opinion, chlorophyll a and b's absorption spectrum is important because it explains why most plants are green. (A lot of people think plant leaves absorb green light making them green instead of reflecting/transmitting the green light back and absorbing the rest.)—Love, Kelvinsong talk 21:03, 8 September 2013 (UTC)

Plantsurfer and 512bits, both of you should not feel bad at the recent "oppose" votes at FAC. Take the advice for what it's worth and continue improving the article (the FAC process, like any other review process, is meant to find flaws). If this first candidacy does not go through, follow the suggestions and try again in two or three weeks.--MarshalN20 | ^Talk 22:32, 8 September 2013 (UTC)

That plants are green because of specific molecular absorption spectra seems to be a sticking point, in fact all molecular information is a sticking point to one or two of the main editors of this article, so there appears to be no way to get off of molecules and onto botany. Plant biochemistry is a major part of botany, and plant biochemists study chlorophyll molecules because they absorb light energy. They can't use all of the sunlight that hits the leaves, only specific wavelengths; the light that they don't use is largely reflected back and this reflection makes the leaves green. We're not training biochemists; we're writing a general article about the field of botany. But, in this article, we have no room to discuss the field, because of the molecule dump. In addition, this molecular dump is problematic because some of it is wrong. --(AfadsBad (talk) 00:34, 9 September 2013 (UTC))

A good critique from the nomination page

So I see that this article has been nominated already, and I saw a comment worth reposting here:

"Oppose Basic question: what is this article about, botany or plants? After the History section, the article goes on extensively about plants—their importance, their internal chemistry, their genetics, how they interact with the environment and how they are classified. But all this belongs to the plant article. The focus of this article should be the meta-aspects (for want of a better phrase) of botany. For eg: how is botany subdivided? (it is telling that branches of botany is relegated to the See also) what are the different approaches to studying it (for eg social sciences have a structuralist approach and a Marxist approach etc)? Are there any ongoing debates? What are the major prizes awarded for stellar work in botany? And so on.—indopug (talk) 14:05, 8 September 2013 (UTC)"

This is something I noticed for a while but had no clue how to fix, so I went along with it, duplicating the Plant article. Of course not working in the field, I know almost nothing about the meta aspects, but User:Indopug has a few good suggtions someone should write about. I suppose organizations like the ASPB and journals like Plant Physiology and The American Journal of Botany should be mentioned too.—Love, Kelvinsong talk 21:17, 8 September 2013 (UTC)

Plant anatomy and morphology

Well, considering I wrote most of this section I'm sad to see it go, but applying fresh scrutiny to it, I don't think it belongs here. I move to cut it and replace it with a shorter section on plant cultivation (Descended from the part on Saintpaulia and asexual propogation).—Love, Kelvinsong talk 21:40, 8 September 2013 (UTC)

I oppose this most strongly. The solution is not to go around cutting stuff from the article, but to consider whether the presentation of the existing material can be improved to bring it into the required focus. If it cannot, then it must be removed of course, but we need to consider carefully every proposal to cut. The article contains excellent material, and I think it would be an act of vandalism to wreck it. I think you should consider the role of Plant Anatomy and Morphology in 19th and early 20th century botanical research. It was a dominant theme. Botany departments were built with the concept in mind that a botanist needed space for his(her) microscope. Labs were for teaching. That change could, should, be reflected in the section perhaps, but to remove the section is inappropriate. Please, let us reflect, discuss and move forward with consensus. Plantsurfer (talk) 08:22, 9 September 2013 (UTC)

The article does contain excellent material on a variety of topics, much of which might work well in other articles. However, it has missed its topic by a long way, and needs material removed that is more appropriate for other articles to make room for the botany article. Yes, anatomy and physiology were dominant topics in botany, but what we should be telling readers, when, how, and why different aspects of boany dominated the science, not teaching them botanical anatomy, physiology, and chemistry in this article. --(AfadsBad (talk) 23:00, 9 September 2013 (UTC))

Close the FAC

It clearly won't pass as people don't agree on what the article should be, so we should just close it and stop wasting our time. I did not spend months and over 1000 edits to see the article gutted. 512bits (talk) 20:20, 9 September 2013 (UTC)

Yes, it is probably better not do an FAC if you have ownership issues with the article. --(AfadsBad (talk) 22:55, 9 September 2013 (UTC))

It's high time you stopped being so pompous and sanctimonious. 512bits (talk) 02:01, 10 September 2013 (UTC)