Wikipedia:Featured article candidates/Metabolism

The following is an archived discussion of a featured article nomination. Please do not modify it. Subsequent comments should be made on the article's talk page or in Wikipedia talk:Featured article candidates. No further edits should be made to this page.

The article was promoted 04:34, 30 March 2007.

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Metabolism

A broad overview of the chemical basis of life, dealing with metabolic processes in microbes, plants and animals. Self-nomination. The article is 78 kb in total size with 43 kb of readable text. It has recently been peer-reviewed. TimVickers 19:16, 25 March 2007 (UTC)

• Comments Dr pda returns less (34KB) prose size; oh, my, those External links! SandyGeorgia (Talk) 02:59, 26 March 2007 (UTC)

I've also just added a "Further reading" section. TimVickers 04:06, 26 March 2007 (UTC)

• Support After reading this article for peer-review (along with Zephyris and BirgitteSB), I'm more than convinced it meets FA criteria. It is comprehensive and not long-winded, uses summary style throughout as needed, is very lay-accessible in my humble opinion and is nicely illustrated, something I find important for such a topic (ooh, pretty pictures! ;) Fvasconcellos 14:37, 26 March 2007 (UTC)
• Support very well-written and well-organized, as usual ;) A few comments:
  • Examples of proteins: fibrous and globular, but not membrane proteins? I know they're just examples, but it's still an odd omission.

Added transporters.

• • I like the glucose animation, but can it be slowed down a bit? I'd be surprised if anyone watching could follow what was going where without watching many iterations.

I can't do that myself, but there is Image:Glucose Fisher to Haworth.gif, would this be an improvement?

I think the one in the article is 'nicer' - the animation is smoother, and there's no weird antialiasing issues when it rotates - but hard to 'get' without watching for a long time unless you already know what's happening. It's up to you - I thought there was a way to set the frame rate for an animated GIF, but I also know nothing about animations. Opabinia regalis 06:40, 27 March 2007 (UTC)

I've put this in as a request to the Wikipedia:Graphic Lab. TimVickers 15:27, 27 March 2007 (UTC)

...and then withdrawn it, since I worked out how to do it myself. Slower animation substituted. TimVickers 20:58, 27 March 2007 (UTC)

• • These section headings seem a little strange: why 'coenzymes' by themselves, and then group cofactors with minerals? The latter is almost all about inorganic ions anyway. Also in this section, the first sentence ending with 'minute concentrations' could mention that these are nevertheless crucial; currently the importance of trace elements doesn't come up till the last paragraph.

Reworded. Coenzymes are separated from cofactors as these two classes of molecules play very different roles in metabolism. I wanted to emphasise this difference as it is not usually discussed well in textbooks.

• • 'The amino acids or sugars released by these extracellular enzymes are then pumped into cells by specific active transporters' - mention that the transporters are proteins.

Reworded.

• • In the proteins section, there's no definition or wikilink to alpha-keto acid, and I wouldn't expect that to be something most readers are familiar with. Actually, in the nucleotides section, the same for 'pyrimidine' and 'purine' - just a link to pyrimidine etc. would be good, as I think the distinction is described earlier.

There's a link in "The amino group is fed into the urea cycle, leaving a deaminated carbon skeleton in the form of a keto acid." was this the section you were meaning? Purine and pyrimidine links added.

• • Three notes numbered in the hundreds is long and crowded in the text - maybe condense refs 119-121 to one note, since they aren't reused.

Done

• • Are any of the images unusually large in file size? This page loads rather slowly for me, though other pages are loading normally.

I don't think so, this is 81kb in size now. Perhaps we should remove the animation?

No, I like the animation - I'm the only one with the problem so far. Opabinia regalis 06:40, 27 March 2007 (UTC)

• • All of the external links seem to be well-chosen; this section is long, but useful. Opabinia regalis 01:06, 27 March 2007 (UTC)

Thanks! TimVickers 03:30, 27 March 2007 (UTC)

• Support -- quite well written--ppm 22:54, 27 March 2007 (UTC)
• Support (non-expert). This isn't an overview of or introduction to metabolism that is fully accessible to the general reader. However, such a big topic would probably require an article the size of a book to achieve that. Reading through (which took me over an hour) I did learn and I was amazed at the complexity of life. I dare say that if I concentrated on a section and followed more of the (over 600) wikilinks I could learn a fair amount. The technical words and phrases are all wikilinked – it is great that there are so many articles to support it. Colin°^Talk 13:12, 28 March 2007 (UTC)
• Support This is very difficult subject to cover in a general encyclopedia article. Well done!--BirgitteSB 13:25, 28 March 2007 (UTC)
• Minor suggestion:

• Nucleotides act as coenzymes in several important group transfer reactions. (a reference would be great)

Anyway I'm going to support it as a perfectly referenced, well illustrated article. Really one of the best works of Wikipedia. Well done, Tim! NCurse _work 20:15, 28 March 2007 (UTC)

Added specific ref for this and a general textbook ref for several other things in this introductory section. TimVickers 20:47, 28 March 2007 (UTC)

• Support: Thank you! NCurse _work 21:26, 28 March 2007 (UTC)
• Comment. "Multicellular elephants" sounds a bit strange. It forces one to contemplate the existance of unicellular elephants, if only breifly. Not sure how one would rephrase that sentence though. Kaldari 01:17, 29 March 2007 (UTC)

Slight rewording to "...the unicellular bacteria Escherichia coli and huge multicellular organisms like elephants." TimVickers 03:35, 29 March 2007 (UTC)

• Conditional support. A great science article that includes substantial scientific detail (or summarizes and links to more detailed pages for those who care) but also in a style and with enough introductory material that makes it accessible to non-scientists as well. Couple of concerns:
  • Image placement quirk: images are in the section before the section describing them, relying on layout/wrapping to place their associated text next to them. At best, that "works, sort-of, on most standard browsers". Better to place the image in the relevant section. I fixed one case, but it looks like a general problem throughout the article.

I've moved the right-aligned images down, but this is the best option for the left-aligned images in subsections. If you put a sub-heading over a left-aligned image then it is separated from the text it refers to and looks like it is a title for the image.

• • Image+table layout problem: a left-side thumb followed by a table forces the table to be to the right of the image, even on narrow monitors. That means side-scrolling...yuck :( Fixed.

Thanks.

• • Fisher projection problem: In the ring/chain image, the convention for a Fisher projection is to place the backbone vertically—otherwise the implied stereochemistry is confusing (and may even be enantiomer for this specific case).

Replaced with different animation.

• • Anabolism intro section confusion: The text describes two types (autotroph vs heterotroph), the flowchart finds six types, and the table has four. Are photoautotroph and chemoautotroph subtypes of autotroph, or is "autotroph" a completely separate thing, or is autotroph both a superclass and a catch-all/"other" subclass of itself? Would this thing be clearer as a tree with tri-state branching ("light", "inorganic oxidation", "other") from each of autotroph and heterotroph roots? Or as a table with rows for light/inorg/other and columns for auto/hetero? Or is this whole flow-chart un-necessary, since a single additional sentence in the preceeding paragraph could explain it all, like: "Organisms can be further classified by ultimate source of their energy: photoautotrophs and photoheterotrophs obtain energy from light, whereas chemoautotrophs and chemoheterotrophs obtain energy from inorganic oxidation processes."

I never liked that flowchart much - ZAP! It is gone. Your text added. Thank you.

• • Pedantic biblio formatting stuff: Some References and Further reading cites use "and" and some use "&" in author lists, and some use periods after first initials while others do not. There's also some inconsistency in what text is the hyperlink, especially for web publications (Buchner's Nobel lecture, for example), presumably as a result of using "raw" formatting instead of the {{cite}} templates. I wouldn't hold up this FAC for failure to use the templates, but at least need to be consistent if doing it manually sometimes. For articles with a PMID, the PMID automatically links, so an additional explicit url that takes one to the same place seems redundant. Only really makes sense if the article is subscription-only via PMID but is available free from some alternate/reprint site.

I've directly linked only the articles with free full-text access, to make it easier for the majority of the readers who don't have web subscriptions to see at a glance what they can access. Fixed formatting for the journal I found. Unfortunately the book cite template produces a slightly different output than the journal cite! TimVickers 16:55, 29 March 2007 (UTC)

• • Lanosterol synthesis image: The methyls at C13 and C14 look skewed...probably "correct" in a ChemDraw/geometric sense, but would look better being completely vertical instead of slanted due to the 5-membered ring. Also the color-coding is weird...indicates bonds not atoms, so a place where a blue line meets a red one is an atom of indeterminate origin. If we believe the lanosterol page (which is questionable, since the lead structure is wrong?!) biosynthetic and if I follow the colors correctly here, the C14 methyl is the wrong color. DMacks 06:04, 29 March 2007 (UTC)
    • I vectorized the image, so I'll take responsibility for the "skewed" methyl groups—those are due to ChemSketch's auto bond angles, I'll fix them if you like. The color coding wasn't mine, so I'll steer clear of that one :) Also, I can't believe the lead structure in lanosterol is wrong; that's not one of mine, but I'll fix it anyway. Fvasconcellos 15:51, 29 March 2007 (UTC)
      • • Lanosterol fixed. Walking away now... :) Fvasconcellos 18:01, 29 March 2007 (UTC)
      • I'm thinking something like Image:lanosterol-synth.png. Coloring fixed to match monomer origins based on the mechanisms on the squalene and lanosterol pages. DMacks 16:57, 29 March 2007 (UTC)

• I think the original is one possible pathway, as DMAPP and IPP can condense to form geranyl-PP, two molecules of geranyl-PP condense to form farnesyl-PP and then two molecules of farnesyl-PP condense to form squalene. However, several pathways are possible, see link. TimVickers 17:57, 29 March 2007 (UTC)

The above discussion is preserved as an archive. Please do not modify it. Subsequent comments should be made on the article's talk page or in Wikipedia talk:Featured article candidates. No further edits should be made to this page.