Wikipedia:Featured article candidates/Photosynthetic reaction centre

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[edit] Photosynthetic reaction centre

Self-nomination. I started this article 23 days ago with the hope of making a high quality, thorough and scientifically accurate article about photosynthetic reaction centres from plants and bacteria. I have put a lot of effort into creating the article and I have had it peer reviewed; I believe it qualifies as a featured article candidate. The article is very scientific and I was nervous at first that it might be ‘too scientific’ for a featured article, but Ive been assured that scientific articles are welcome on the front page. Miller 18:29, 1 March 2006 (UTC)Image:Signature george.PNG

  • SupportOppose; I would love to see this featured (it sounds like it could be interesting), but using sentences such as "The peak molar absorption coefficient of chlorophyll is 105 M-1 cm-1, among the highest observed amongst organic compounds." without any explanation of or links to molar absorption, and a use of JPEGs rather than <math> statements for equations make the article too difficult at below university level (it makes little sense to an A-level biology & chemistry student like me). smurrayinchester(User), (Talk) 21:00, 1 March 2006 (UTC)
    • I've fixed the formulae up. smurrayinchester(User), (Talk) 21:14, 1 March 2006 (UTC)
    • I'm changing my vote to support, now that this article really looks good! Much improved on when I first saw it... smurrayinchester(User), (Talk) 21:52, 4 March 2006 (UTC)
  • conditional support and commentI think that's a point that need to be raised. Personally I have no problem reading this because of my background, but I think even if appropriate links are provided to explain this concepts, people are still not going to understand it because wikipedia is relatively poor in molecular biology topics (zoology is fine on wikipedia in my opinion), and there is just NO WAY to explain these concepts just through encyclopedia readings; you'll need years of training in sciences to understand most math, engineering, mol bio articles. Granted most people can't tell difference between DNA and protein. That being said, however, I don't think that should prevent it from being featured as FA. Here's some suggestions:
1. Most people don't know about rxn centers, but most of them have heard about photosynthesis. So maybe a couple paragraphs about photosynthesis (in layman's terms) to show where photosynthesis occurs, and what's the ultimae goal of photosynthesis.
2. A paragraph about what a photon is, and how it carries energy. Also, how a molecule can absorb or release energy when hit by photons. And how is it relevant to photosynthesis.
3. People are not going to understand what electron donors or acceptors are, so maybe need to give them first an idea: why and how when an electron falls down a gradient potential can energy be amassed and used? What's the point of falling down a gradient?
4. Before going into details about plant and bacteria, talk about evolutionary relationships between them. Also say where in cells are these systems found.
comments: most of information you can probably find in textbooks, so paraphrasing and then cite at end should be fine. One thing to make this more complete is maybe link to people who've done research on this. I know it maybe hard, pubmed rarely gives pdfs for research done in 50s or 60s. But I'd like to see some primary research at reference section.
finally, science topics are almost always harder to understand than humanities, but I don't think it should be the reason to keep it away from gaining FA status. I'll give more comments if needed. Temporary account 23:17, 1 March 2006 (UTC)
  • Weak ObjectSupport- not ready yet, needs more work. There is a lack low amount of inline citations, critera 2(c). Though I don't mind the level of "scientificness" (even if it is mostly too difficult for me also), I think it would be better if it would be toned down a bit in terms of that. References need to be cited correctly (I'll work on that). I would also prefer a more hierarchal structure to the TOC (3b). Though people familiar with the topic can immediately realize that the two photosystems are in the chloroplasts of green plants, what about other less familiar people? They would be unable to discern that the photosystems didn't exist in the bacteria. Instead, it should be of similar format, with the paragraph under "Bacteria and plants" moved up to the lead, and three separate sections be created: Bacteria, Algae, and Plants. (Both photosystems would fall under plants). AndyZ 21:18, 1 March 2006 (UTC)
  • Comment I was afraid that certain terms might make the article hard, if not impossible to understand. If you can pick out examples of this, please leave a message on my talk page and I'll add an explanation or change the wording to make it more understandable.Miller 21:56, 1 March 2006 (UTC)Image:Signature george.PNG
    • While I was suggesting that it should be simpler- I didn't mean that much simpler- just meant like explaining stuff with more detail, not with sentences like "Imagine balls sitting on top of different steps on a flight of stairs". thanks, AndyZ 01:00, 2 March 2006 (UTC)
  • Object Let me begin by saying that I applaud your swift accomplishment. Few articles look this good after a year of work. I second the request for inline citations and agree with the suggestion to add more basic background. While it's impossible to gain a working understanding of advanced scientific concepts without years of university study, a good writer can convey basic principles and general concepts to any educated reader. Isaac Asimov made a career of that and I recommend Miller review some of Asimov's essays as models for how to introduce complex topics to a broad audience. Wikipedia's space limits provide plenty of room for this article to expand. You've demonstrated your ability to write fine prose swiftly so I think you can address these concerns within the nomination period. Add a background section to bring a nontechnical reader up to speed, then offer a high level analysis of significant concepts with their function and and significance. Ideally this would prepare some readers to at least skim the graduate level technical discussion that concludes of the article. Best wishes, Durova 23:57, 1 March 2006 (UTC)
    • comment I have to disagree on this one. Science fiction is different from real working of science. There are scientific subjects which really require solid background in sciences to understand. And this is through my own experience. Imagining explaining transcriptional regulation of hormone receptors and reporter assays to university seniors of humanities majors. That was a gigantic pain in the ass, and I know this from first hand experience. If you want to explain this article so everyone understands, either these explanations will be longer than the article, or that you will leave out lots of points. However, I do want to point out for articles like this, we need non-laymen to do a thorough review. Temporary account 00:09, 2 March 2006 (UTC)
      • Actually Asimov wrote much more than just science fiction. He was the most prolific writer of all time. He even provided one of my first introductions to astronomy in a nonfiction children's book I read when I was ten years old. Since he can explain light years and quasars to elementary school children, I'm pretty confident there are techniques you could adopt from his style. Durova 00:33, 2 March 2006 (UTC)
        • We'll all help to make the articles as approachable as possible. But I have a feeling that this particular article is really hard. Photosynthesis is easy (H20+CO2+light->sugar!), but rxn centers are hard. Same thing, easy to understand Newtonian physics (a ball thrown upward will come down the same speed you throw it up), but quantum mechanics are hard. Astronomy is easy, fusion reaction within stars is difficult....etc. Something just require some background to understand, and not everything can be explained without solid prior knowledge. Temporary account 00:46, 2 March 2006 (UTC)
  • Comment I’ve prepared a new section laying out the principles behind photosynthesis, but it’s very erratic and poorly written. If anyone can clean up the section and integrate it into the article in an appropriate fashion I would be greatly appreciative.

==The process of photosynthesis==

The various concepts and the structure and functioning of all the different proteins and other molecules that are involved in carrying out photosynthesis are diverse and very complicated. A simple definition of the process of photosynthesis might be ‘the capture of light energy and conversion into chemical energy’. The chemical energy in question is food, in the form of sugar, for the organism in which is carrying out photosynthesis.

Photosynthesis provides food directly for green plants and many bacteria and algae and provides food indirectly for every other form of life on Earth. It is clear that photosynthesis originates from simple bacteria in the very early stages of evolution. Green plants have chloroplasts inside them which, as well as containing the photosynthetic apparatus, also contain their own DNA and the necessary machinery to synthesize proteins. It is though that a photosynthetic bacterium was ‘swallowed’ by another cell and remained alive in the host cell.

This ‘original’ photosynthetic bacterium is believed to be an ancestor of a cyanobacterium. Evidence suggests that chloroplasts from higher plants and green algae are derived from the same event, whereas those in red and brown algae arose from at least one more additional event.

In the course of evolution many of the genes from the original bacterium’s genome where transferred to the plant’s nucleus, the storage site for the plants genetic material (DNA). Miller 01:27, 2 March 2006 (UTC)Image:Signature george.PNG

  • Weak support. The readability of the article is a bit daunting at times, but I was able to grind my way through most of it. I don't think the level of 'scientificness' will be an issue, because this topic is quite obscure. Anyone who comes to this article looking for information probably already knows what they are looking for specifically and already possesses some background knowledge of the topic. Inline citations need to be added, but I trust that this can be done in a timely manner. RyanGerbil10 03:29, 2 March 2006 (UTC)
  • Weak oppose. First off, it needs a copy edit, so that all the sentences end with the proper punctuation and so forth. For this sort of topic, I don't think we need to be fanatical about inline citations, but the reader should be able to track specific numbers and figures to a verifiable source. Anville 10:49, 2 March 2006 (UTC)
    • I added a couple of inline citations, and plan on doing more later. AndyZ 22:03, 2 March 2006 (UTC)
      • I went through and copyediting the spelling mistakes- don't know about punctuation though. AndyZ 22:40, 2 March 2006 (UTC)
        • It doesn't seem that any of the sentences end with improper punctuation- they all end with periods. AndyZ 02:14, 5 March 2006 (UTC)
  • Oppose. It lacks inline references, which is now one of the "hard criteria" for an FA. - Samsara contrib talk 11:30, 2 March 2006(UTC)
    • I added a couple of inline citations, and plan on doing more later. AndyZ 22:03, 2 March 2006 (UTC)
      • Thanks for reacting to my concern. I think it would be good to have a few more peer-reviewed references (i.e. from peer-reviewed journals) or at least printed ones, e.g. textbooks. You should reference them fully, title and ISBN is not enough. I don't particularly like this reference game, because people often look at the number of references rather than whether the controversial or novel-sounding points are supported by references, but everybody's being treated by the same rules (i.e. we're all just imitating each other), for instance see my peer review of tuatara. Thanks. - Samsara (talk • contribs) 11:12, 3 March 2006 (UTC)
        • I added as much information as I could find to the citations/references, and there is one textbook, except it is online. I will add my own biology textbook as a reference though if needed to verify anything. AndyZ 23:40, 3 March 2006 (UTC)

One suggestion is to write this article like scientific review article in peer-reviewed journals. Usually in these reviews, when a claim is made, right after the sentence will have (authors, year) and in the citation section they will have full article name, journal name, authors, year...etc. One thing that concerns me is whether citing textbooks as in-line citation is a good idea. In writing scientific articles (such as in Cell or Science), rarely is a textbook ever used as a source. Usually only primary research or other review articles are cited. I guess that will require lots and lots of pubmed search. Temporary account 18:24, 2 March 2006 (UTC)

  • I'm on it. Give me a few hours and I'll get the sources I need.--Miller 18:59, 2 March 2006 (UTC)Image:Signature george.PNG
It's closer. I really recommend you browse some good science populariations: Lewis Thomas, Stephen Jay Gould, etc. You lose the nontechnical reader in the first paragraph. That would be fine for a science encyclopedia, but not here. Durova 19:20, 3 March 2006 (UTC)

What do you believe is still needed?

  • More inline citations (which sections?)
  • On complex scientific principles :

Remove certain parts
Provide appropriate references
Explain them in more detail
Rewrite these sections

  • Grammar, syntax, layout etc

--Miller 21:45, 3 March 2006 (UTC)Image:Signature george.PNG

  • Comment Generally speaking, I've noticed that the best science popularizers put a human face on their subject—not just literally, as in Gonick and Wheelis's Cartoon Guide to Genetics, but in a metaphorical way. Reading some good Asimov gives one a sense of human drama: at first we are ignorant, then somebody gets an idea, by a long shot it works out and we illuminate one more tiny, fascinating piece of the natural world. Many textbooks appear to be shallow on this "historical" treatment, partly because knowing the history of science doesn't help the student solve exam problems. This blindness is detrimental to all concerned: for those students who actually go on to become scientists, learning how a scientific model gets invented and tested is invaluable. Moreover, the many students who don't go on to be professional, workaday physicists or biologists—the ones who take classes because they're course requirements—miss receiving the sort of knowledge which could actually make science meaningful for them: the perception of science as a human endeavour.
So, how to save the world with a Wikipedia article? A good first step would be to give a good coverage of the way photosynthetic reaction centres were discovered and explored. In a really solid article, one which truly deserves the Featured star, I'd expect to see sentences like "The reaction centres in R. pinkfloydi bacteria were a mystery, until a team of researchers led by Fred Foobar managed to work out their molecular structure. Foobar and his colleagues used X-ray diffraction to understand the shape of the reaction centre molecules..." I'm making up the details, of course, but does the general idea make sense?
This is the sort of knowledge that I believe a good article should supply. There are plenty of copy editors, footnote adjustors and prose brilliantifiers running around the Wikipedia, so if the article has the necessary knowledge it it, the rest will follow naturally.
Anville 09:10, 4 March 2006 (UTC)
Excellent point. A comprehensive science article should include history of science. Durova 19:17, 4 March 2006 (UTC)
Agree also, and some history has already been added to the article. Thissite also has many links to sites that discuss the actual history of photosynthesis, which might be helpful in this task. AndyZ 13:44, 5 March 2006 (UTC)
  • Oppose due to image licensing problems. --Gmaxwell 23:29, 4 March 2006 (UTC)
  • Finding appropriate images with or without big brother (AKA Rhobite) watching over you is hard. Can somebody who is good at finding usable images help me out here?--Miller 00:44, 5 March 2006 (UTC)Image:Signature george.PNG
    • Look, you're the one who came to me for help. I ignored your snarky comments ("You seem to enjoy deleting images") and patiently explained to you why Wikipedia doesn't allow you to use images with restrictive licenses. But in the above comment, you appear to be admitting that you would ignore Wikipedia's copyright policy if you thought you could get away with it. I am trying to protect Wikipedia's legal status and promote the cause of free content. I don't appreciate being called names by someone who doesn't respect the intellectual property of others. Rhobite 01:00, 5 March 2006 (UTC)
      • How did you pick that up within 16 minutes of it being written?!!! Scary. Sorry about that, I wasn't calling you names, just having a laugh - somebody who didn't like what I put on the Jeremy Glick page accused me of being a pedophile! The comment is still on the discussion page if you don't believe me. The point I was trying to make is that I'm not very good at finding apropriate images and I'm looking for help.--Miller 01:40, 5 March 2006 (UTC)
        • Perhaps you might want to consider Fair use images, as long as you can provide the fair use rationale. AndyZ 01:45, 5 March 2006 (UTC)
          • Sorry, but the new image with the chloroplast lacks a fair use rationale, and therefore doesn't fit in with the copyright policy either. That rationale needs to be added. AndyZ 02:00, 5 March 2006 (UTC)
            • I think I'll just give it up as a bad job! I guess you cannot but try.--Miller 02:06, 5 March 2006 (UTC)
              • I added a fair use rationale which I believe works (again, can somebody please double-check). For the other image that has no copyright tag, I have temporarily removed it from the article using HTML comment tags until if a suitable copyright tag can be found. AndyZ 02:11, 5 March 2006 (UTC)
  • Actually there may be a clean and easy (if somewhat slow) solution. How about e-mailing a couple of researchers in the field and asking them to grant Wikipedia permission to use their image? A typical scientist would be pleased and flattered by the request, I think. Durova 03:08, 5 March 2006 (UTC)
    • I'm going to second that suggestion. I see that the situation has been improved some since my initial objection, but it's not enough the lead image is still a 'fair use' image. I'm going to take a hard line on this one: I will object to the featuring of this article until it is free of unlicensed copyrighted material. Fair use is acceptable when we're talking about a copyrighted work, but there is no copyrighted work under discussion here, there is no reason why this article can't be 100% free content. I can't argue that this is the best we have to offer when it makes unnecessary use of 'fair use'. Also, the 2D diagrams in the article should be SVG's the jpeg artifacts make them look terrible. As a gesture of good will (after all, I'm opposing right now) I've replaced one of the two with a SVG, and will get the other one later. --Gmaxwell 20:49, 6 March 2006 (UTC)
  • Oppose i have been editing this article recently. i just discovered it is an FA candidate. I think this is a little premature.
  1. There is a lot of redundancy in the article. i have tried to prune that down a bit.
  2. The cartoons could do a much better job. For example, where are the H, L and M subunits in the bacterial reaction center cartoon? Where is the periplasmic space vs the cytoplasm.
  3. The history section does a poor job of relating Priestly's work to the topic of reaction centres. i tried to fix this but it needs more work.
  4. There was a lot of information in the article that was peripheral to the topic of the article. i have tried to delete some of it.
  5. Problems with nomenclature. For example, "special pair" was over used especially since it was defined as P960 in the bacterial section.
  6. I still feel there is a lot of work to make this article have the context required for a FA article. For example, several of the wiki links were not that informative (cyclical and soluble) and others that could have pointed to great wiki articles were missed ( cytochrome b6f complex)
I have tried to address some of the issues above but the article still needs a lot of work. David D. (Talk) 20:33, 7 March 2006 (UTC)
  • About the image, it was taken from the Protein Data Bank, and to show the structure of the perisplasmic space vs. cytoplasm would be difficult to do. As for the history section, agree that everything is not very well related with reaction centre. Priestly's work deals with the discovery of oxygen, not the reaction centre, so they draw very weak relationships- that definitely needs to be cleaned up. I think "special pair" refers generally to the pair of chlorophyll molecules that exist in the photosystems. AndyZ 21:17, 7 March 2006 (UTC)
    • I just updated the diagram to try and give a more general picture of what is going in with regard to the bacterial photsynthetic reaction centre. See the talk page for the article. I understand what the special pair refers to but why can't we call them the P960 (or P680/P700)? Just to clarify there are chorophylls in these photosystems that are not anything to do with the reaction center "special pair". David D. (Talk) 03:48, 8 March 2006 (UTC)
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