Wikipedia:Featured article candidates/Archaea

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 by User:SandyGeorgia 02:47, 2 July 2008 [1].

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Archaea

Self-nominator: Tim Vickers (talk) Co-nominator: EncycloPetey

Overview of one of the three Domains of life, and a companion to the featured article on Bacteria. Of top importance to Wikipedia's coverage of biology and classified as a vital article by the Version 1.0 Editorial Team. Tim Vickers (talk) 17:12, 25 June 2008 (UTC)

• Support However, Cofactor and Micrometer lead to disambiguation pages. Gary King (talk) 17:36, 25 June 2008 (UTC)

I've disambiguated these links. Tim Vickers (talk) 19:04, 25 June 2008 (UTC)

Comments

• What makes http://tolweb.org/tree/home.pages/abouttol.html a reliable source? Note, biology isn't my field, so it very well may be, I just haven't ever heard of it. (current ref 38)

The article used on that website is one of the essays written by named, expert contributors, so I think that passes WP:V, although not all the content of the site would do so.

Although some parts of the site are bare or poorly maintained, other parts have extensive research and references. The project is written and coordinated by leading experts in the field of systematics, with various groups of organisms overseen by their respective specialists. --EncycloPetey (talk) 03:23, 26 June 2008 (UTC)

• The link checker tool is showing that the pnas.org links are down, but they are working if I click through.

Odd.

Does that sometimes. Figured I'd point out the oddness, but also point out that the links are working for other reviewers. Ealdgyth - Talk 18:36, 25 June 2008 (UTC)

• Current ref 62 "Based on PDB 1FBB" is lacking publisher and last access date.

Ref added. Tim Vickers (talk) 18:30, 25 June 2008 (UTC)

Otherwise sources look good. Links checked out with the link checker tool. Ealdgyth - Talk 18:24, 25 June 2008 (UTC)

All done! Don't expect me to review the prose... biology articles make my head hurt. Give me a nice ancient history article any day... Ealdgyth - Talk 18:36, 25 June 2008 (UTC)

Comments: Wow, what an interesting article! Looks great Tim, but on first read through, I picked up a couple of minor things:

• In the lead, there is a sentence (below) I'm stuggling with (my poor language skills, I'm sure!). I'm not sure whether it should mean "archaea carry out photosythesis", or "no known archaea carry out photosynthesis" or "no known archaea carry out photosynthesis in addition to fixing carbon and using sunlight"

Salt-tolerant archaea (the Halobacteria) use sunlight as a source of energy, while other species of archaea fix carbon, but no known archaea do both and carry out photosynthesis like plants and cyanobacteria.

Reworded to "Salt-tolerant archaea (the Halobacteria) use sunlight as a source of energy, while other species of archaea fix carbon, but unlike plants and cyanobacteria, no species of archaea are known that can do both." - apparently in the specific usage photosynthesis refers only to the use of sunlight to capture carbon - so only if you do both are you technically a photosynthetic organism. It's probably clearer without mentioning this.

• In the Origin and early evolution section, last paragraph - is the word analyzes correct? My mind wants to read analyses.

That's me trying too hard to speak American!

I sympathize - welcome to the league of Brits that have forgotten how to spell ;o)

• The Cell membranes is a little too technical with some unexplained/unlinked terminology (acyl chains, sn-1, sn-2 etc.) Is there any way of directing the reader to explainations of these terms?

That much detail isn't really needed. I just removed it. Tim Vickers (talk) 20:09, 25 June 2008 (UTC)

best of luck, ~ Ciar ~ _{(Talk to me!)} 19:14, 25 June 2008 (UTC)

• Support - my queries were addressed in full! ~ Ciar ~ _{(Talk to me!)} 20:15, 25 June 2008 (UTC)

• Support So satisfying in every respect, not least because of all those blue archaeal genera. ;) Some technical points are listed below; well done, Tim! :) Willow (talk) 21:19, 25 June 2008 (UTC)

Perhaps be more specific about the isoprene compounds that were used as chemical fossils? Readers might get confused because isoprenoids show up in almost all branches of life, e.g., squalene and farnesyl transferase. Willow (talk) 21:19, 25 June 2008 (UTC)

Clarified and condensed. Tim Vickers (talk) 22:20, 25 June 2008 (UTC)

Mention the community aspects of archaea in the lead? You know, all that stuff about biofilms, cannulae, etc.? That seems important to me, that they can do even more complex things by bouncing off of one another. Willow (talk) 21:19, 25 June 2008 (UTC)

Expanded the second paragraph of the lead. Tim Vickers (talk) 23:20, 25 June 2008 (UTC)

The description of their phylogenetic tree could be made clearer? The major phyla come only at the end; we're not seeing the forest for the trees (genera). Willow (talk) 21:19, 25 June 2008 (UTC)

Paragraphs re-ordered. Tim Vickers (talk) 23:20, 25 June 2008 (UTC)

Can you say something more about the word archaebacterium mentioned in the lead? When was it introduced by whom; when did it fall from favour and why? Willow (talk) 21:55, 25 June 2008 (UTC)

I've added an explanation of why it was coined and why it isn't used any longer. Tim Vickers (talk) 23:20, 25 June 2008 (UTC)

It might be nice to read about the traits that bacteria, archaea and eukaryotes share? For example, is the composition of their cytosols more or less the same, e.g., similar pH, similarly reducing environment, etc.? I'm guessing so, since some of their enzymes are related and maybe would need a similar environment to function similarly? On the other hand, I think I've heard that hyperthermophilic archaea have some characteristic adaptations to their environment, so maybe there aren't many common traits. Willow (talk) 21:55, 25 June 2008 (UTC)

This is a tricky one, since I can think of a huge lest of chaacteristics that are shared between all forms of life - DNA, protein-based enzymes, reducing cytosols etc.. but can't really see listing these in each article on specific forms of life. For instance, I wouldn't mention in an article on squirrels that tey have a DNA-based genome. However, I do agree that so much is focussed on what divides archaea from other organisms that the similarities are not emphasised. I've added an introductory papragraph to the "Cell biology" section to discuss the similarities before the article launches into the differences. Tim Vickers (talk) 23:20, 25 June 2008 (UTC)

Under "Significance in technology and industry", I seem to remember hearing that hyperthermophilic archaeal proteins were good for X-ray crystallography and structural genomics, since they're more stable at room temperature? But I'm not sure if that's actually true; I'll try to find a reference. Willow (talk) 21:19, 25 June 2008 (UTC)

They're also satisfyingly easy to purify - you extract your E. coli by boiling! Tim Vickers (talk) 21:34, 25 June 2008 (UTC)

I've added a sentence on structural biology to the Technology section. Tim Vickers (talk) 23:28, 25 June 2008 (UTC)

Comments: While the article hits most of the important topics which spring to mind, I'm not sure it is yet at Featured. Some examples: (1) "However, a new approach was proposed in 1965,[2] in which microbiologists examine the sequences of the genes in these organisms and use this genetic information to work out which prokaryotes are genuinely related to each other." and the following sentences seem kind of wordy. Maybe something like, "However, as molecular phylogeny data became available starting in the 1960s, it became clear that the archaea and bacteria formed two distinct lines of prokaryotes". I would trim back all the prose about now-discarded terminology, the history of molecular phylogeny, etc (especially since it appears in many parts of the article, not just one). I know you added some of that in response to feedback on this page, but perhaps there is a way to mention these things without taking so many words (or just snip out some of the more peripheral aspects). (2) Although the text "The Archaea should not be confused with the geological term Archean eon, also known as the Archeozoic era. This refers to the primordial period of earth history when prokaryotes were the only cellular organisms living on the planet" probably should not be removed entirely, it really makes for a poor lead-in to "Probable fossils of these ancient cells". (3) The whole paragraph "The classification of archaea . . . from other such groups" is belaboring points which are tangential. Some of these can be touched on, but it should be more in passing, briefer, and more in the context of what it means for the Archaea. (4) The discussion of the internal classification could be slightly expanded, with at least a few hints of why the classification was made, what distinguishes the phyla ("most Crenarchaeota lack histones" or whatever seems to make sense), and which aspects of the classification seem (relatively) well established. Now, having said all that, there's lots of informative, well-written text here. So this isn't really an Oppose even if some passages didn't read as well for me as it seems like a Featured Article should. Kingdon (talk) 04:49, 26 June 2008 (UTC)

• I've condensed and tightened the Discovery section.
• I've cut that piece about the Archanean era. I might put it back somewhere else but it is a digression. Tim Vickers (talk) 15:49, 26 June 2008 (UTC)

  I've moved the bit about the Archean era to a disambiguation tag at the outset, modelled after the one appearing at the top of the Archean article. --EncycloPetey (talk) 16:23, 26 June 2008 (UTC)

• I've added a sentence on molecular phylogenetics to the classification section, since this is the basis of most of these classifications. Tim Vickers (talk) 17:18, 28 June 2008 (UTC)

Support Oppose for now on accessibility and jargon. I was so excited to read this article because I've been a reading a popular science book about cell biology that rhapsodizes over the importance of the discovery of archaea. So, I thought - I'll learn more about them! Yeah! Unfortunately, I did not really learn that much. This article was hard to follow for the layperson. My roommate and I read it aloud during dinner, clicking on things we didn't know and trying to figure out what was being said (and he's even taken some biology classes!). I think that the article assumes a familiarity with biological terms and concepts that most people do not have - it needs to do some more explaining to the rest of us! Here are some examples:

• The difference between prokaryotes and eukaryotes is never described. I'm not sure how common this knowledge this and the lead assumes it from the very first sentence.

Good point, now added to the lead. Tim Vickers (talk) 17:19, 26 June 2008 (UTC)

• A great deal of the article is spent comparing Arachaea to the other two domains - how they are the same and how they are different. Why not just describe the Archaea? My roommate speculated that this is because we know so little about Archaea, so all we can really do at this point is compare. At any rate, the comparisons are hard to understand without a firm grounding in the other two domains.

• Let me dissect a section and show you what someone like me, a layperson interested in science but not trained in it, gets out of the material (I have inserted my thoughts in red - I hope you find them amusing in a way):

"Archaeal membranes have a distinctive composition. Like bacteria and eukaryotes, archaea possess glycerol-based phospholipids called ether lipids.(lipids are fats, right?; ether is not the outmoded aether theory and not the thing that puts to you sleep, presumably, hmmm - I wonder what it is - ok "some sort of lipid called a lipid") However, three features of archaeal lipids are highly unusual:

• The archaeal lipids are unique because the stereochemistry of the glycerol is the reverse of that found in bacterial and eukaryotic lipids - the glycerol components of these lipids are mirror images of each other - they are enantiomers. (I am going to assume "stereochemistry" is "chemistry"; what's glycerol again?; glycerols are mirrors - why is that important? I'm missing something here.) Since most synthetic enzymes (Why are we talking about synthetic enzymes? Is something here an enzyme? Why is it synthetic? I bet that doesn't mean "human-constructed" here! I am so stupid) are stereospecific for one enantiomer, this is strong evidence for a different biosynthetic pathway.(I am now totally lost)

• (Breathe, perhaps you will understand point 2) Most bacteria and eukaryotes have membranes composed mainly of glycerol-ester lipids, whereas archaea have membranes composed of glycerol-ether lipids.(ester vs. ether? why does this difference matter?) Even when bacteria have ether-linked lipids, the stereochemistry of the glycerol is the bacterial form.(What?) These differences may be an adaptation on the part of archaea to hyperthermophily. However, it is worth noting that even mesophilic archaea have ether-linked lipids.(Why is that worth noting? Does that mean it may not be an adaptation for heat loving?)Main point: Archaea have membranes composed of a certain type of lipid. This matters for some reason.

• (Third time is a charm!) Archaeal lipids are based upon the isoprenoid sidechain.(What's the isoprenoid sidechain?) Only the archaea incorporate these compounds into the straight-chain lipids in the plasma membranes. In some archaea, these isoprenoid side-chains are long enough to span the membrane, forming a monolayer for a cell membrane with glycerol phosphate moieties on both ends.(Eh? I suppose this monolayer is important somehow? Or is it the moieties, whatever those are?) This dramatic adaptation is most common in the extremely thermophilic archaea.(Oh, yes, so dramatic. It is speaking to me right now. Why thermophilic? I have no clue.)

Main point: Archaea have distinctive membrane features. I am not very clear on what those features are, though.

I know how hard it is to make something accessible when it is one's specialty. If you would like me to go over the article section-by-section on the talk page, showing you things I did not understand, I would be more than willing to do so. As you point out, this is a vital article! Awadewit (talk) 15:15, 26 June 2008 (UTC)

I've rewritten this section, hopefully the new version won't be quite so indigestible over dinner! Tim Vickers (talk) 18:08, 26 June 2008 (UTC)

Yes, I think the section is much improved. However, I still think that the idea of why some of these things are important is getting lost. For example, the ester-ether distinction. Is that interesting because no other life form has that formation and we never knew life could be like that before we discovered archaea? Is it interesting because it shows us how distant the archaea really are from other life forms (they might seem like other teeny-weeny things to people like me, but we should put that out of our heads right now)? Something else entirely related to chemistry that I am missing (I'm only half-way through the MIT opencourseware biology 101 lectures, after all). Awadewit (talk) 20:22, 26 June 2008 (UTC)

OK, I think I see what you're getting at. We've approached this from an evolutionary viewpoint, but have missed out the physiological relevance of these unusual lipids. I've added some material on how these structures may help archaea live in extreme habitats. Tim Vickers (talk) 23:53, 26 June 2008 (UTC)

Your points about the density of scientific terminology are valid, and Tim and I (and probably others) will do what we can to make the prose more accessible. However, I'd like to address one comment you made: "A great deal of the article is spent comparing Arachaea [sic] to the other two domains - how they are the same and how they are different. Why not just describe the Archaea?"

Simply describing features of the archaea is insufficient. Much of the article is written in a "compare and contrast" style, which is a standard means of presenting distinguishing characteristics. This style is necessary for two reasons:

1. The importance of the Archaea as a separate branch of life (one of three) requires that the reasons for recognizing them as separate be explained. This separateness is noted several times at the outset of the article. Thus, simply describing them, without making comparisons and contrasts with other forms of life, would not enable a person to understand or appreciate their uniqueness. Consider that the article could say that membrane lipids of the Archaea are ether-linked. OK, so why is that important or relevant? Is that different or the same as other living things? Well, the relevant information must be presented by comparison with the other two major domains of life to provide the answer. In this case, all other life has ester-linked lipids in their membranes.
2. Archaea are microscopic and beyond the experience of most people, so the additional context of comparison and contrast provides context for mentioning each feature. Diagnosis, by which I mean the recognition of a thing as opposed to other things, of the Archaea requires that one know which characteristics are unique to the thing and which are shared by other things. This then constitutes a definition of the thing. While this is not the only approach possible for presenting a definition, it is the better approach when describing something that is not only beyond the experience of most people, but beyond their ability to perceive directly.

--EncycloPetey (talk) 17:00, 26 June 2008 (UTC)

In principle, I agree with you - I use comp/cont all of the time when I teach, too. The problem is that the reader has to understand what is being compared and contrasted. So, for example, the comparison between ester and ether membranes means nothing to me. I understand that they are different, but I have no idea how. It is not an enlightening contrast. I'm afraid that to the layperson, such a difference sounds, um, rather minor. I understand that it may not be at all - I understand that there may be huge ramifications to the ester/ether distinction, but the article doesn't really explain those in terms that I can understand (and I really do want to understand). I don't come away from the article going "wow! it's amazing that archaea have ether-linked membranes! i mean, all other life forms have ester! how did that evolve? I have to go find out! This is fascinating!" Rather, I come away puzzled about why this distinction is so important. Does this help explain the problem with some of the comparisons and contrasts? Awadewit (talk) 17:19, 26 June 2008 (UTC)

Did I misunderstand your question, then? I understood your question to be "Why are comparisons repeatedly being made in the article, instead of just describing the Archaea without making comparisons?" Was this understanding not correct? That was the question I tried to address with my response above. --EncycloPetey (talk) 17:36, 26 June 2008 (UTC)

That was the first part - the second part stated "At any rate, the comparisons are hard to understand without a firm grounding in the other two domains", which I have tried to expand upon here. Awadewit (talk) 17:46, 26 June 2008 (UTC)

I see your point. In the section on cell walls the old version mentioned that archaea have "S-layers" and that bacteria usually don't, but failed to say what S-layers actually were. In focusing so much on the differnces, thie article sometimes fails to explain the system where the difference is seen. "In archaea, the astebagard is synwise to the bootaleps, while in bacteria this in hubwards to the bootaleps." :) Tim Vickers (talk) 18:21, 26 June 2008 (UTC)

Follow-up: The difficult sections have been edited to reduce jargon and to explain the difficult terms that remain. --EncycloPetey (talk) 22:06, 27 June 2008 (UTC)

Perhaps a tad more work on the "Metabolism" section? Awadewit (talk) 14:13, 30 June 2008 (UTC)

Just a tad?! Nice to know the article has improved that much in your estimation. Tim and I will work on improving the text in that section. --EncycloPetey (talk) 16:21, 30 June 2008 (UTC)

Thanks for keeping on going with this Awadewit! We've rewritten this section a bit more so it relies less on the daughter articles and should serve better as an independent summary. Tim Vickers (talk) 17:07, 30 June 2008 (UTC)

This is much clearer - a big thanks from interested lay people like myself! Awadewit (talk) 02:20, 2 July 2008 (UTC)

Where does Awadewit's Oppose stand? Has she revisited? SandyGeorgia (Talk) 17:48, 1 July 2008 (UTC)

I have revisited and am now supporting. Awadewit (talk) 02:22, 2 July 2008 (UTC)

Support. The article is well-written, comprehensive, and (to me at least) very engaging. I suspect that some reviewers will expect this article to be easy going, given it is about bugs. They will be disappointed. Archae, like bacteria and viruses, are highly evolved and have complex structures and biochemistry. The article uses technical words because this is the only language we have to describe accurately these features. Having said that, the language is easily understood by any reader with a basic grounding in biology and chemistry, (yes, it is the ether that puts you to sleep). The nominator is to be commended for the level of accessibility achieved. I would hate to see the article turned into baby food simply to obtain FA status. GrahamColm^Talk 17:17, 26 June 2008 (UTC)

It is much easier to write on technical topics using technical terms, but I'm conscious that if you write very carefully it is often possible to avoid them or put them in context so that they are more easily understood. I'm working on doing that at the moment. Tim Vickers (talk) 18:08, 26 June 2008 (UTC)

Do I get to plug Wikipedia:Make technical articles accessible here? On the whole, I think this article does a good job of walking this tightrope. In the example of the cell membranes, I like "which might contribute to the ability of some archaea to survive at extremes of temperature and in very acidic or alkaline environments" because it makes the distinction in a way which makes sense for archaea. Another tack would be something like "basic cellular structures, such as membranes, tend to vary little among organisms and the distinctive archaean membrane makes it more different from a bacterium than an animal is from a plant" (well, that isn't great wording, but something like that). I'm less keen on text like "In ester lipids this is an ester bond, which involves two oxygen atoms (labeled 6 in the Figure), whereas in ether lipids this is an ether bond, involving only one oxygen atom (labeled 2 in the Figure)." If people already know this, it is a distraction. If they don't, then trying to absorb this information at the same time that they try to figure out the significance of the two kinds of bonds for archaea is likely to produce mental overload. But anyway, I thank Awadewit (talk · contribs) for providing reactions (it is always good to hear how first-time readers react to an article, a perspective which it is hard to get if you've worked on an article, even if we/they have only read it a few times). There is only so far we can go to make the article easy for this sort of reader (given other goals, like not watering it down), but we should do what we can. Kingdon (talk) 03:48, 27 June 2008 (UTC)

I've simplified that description of ether/ester bonds. Tim Vickers (talk) 18:56, 27 June 2008 (UTC)

Support, which I've been holding back because the article is still being actively improved :) Top-notch references, good use of images, excellent prose (not quite excellent a couple of days ago, but it is now)... definitely FA level in my humble opinion. I must say you've responded admirably to Awadewit's concerns: the article is much more lay-friendly than it was when I last skimmed through it, and has certainly not been turned into baby food (always a concern of mine as well, Graham :) I do have a couple of nit-picks as usual:

• In the lead: "We now know that archaea..."—It is now known, if you please :)

Reworded

• In "Morphology": "Recently, even a species of flat, square archaea...has been discovered." When exactly? The reference is to a 2005 article.

Not so recent, I've found the original ref and this is from 1980. Added ref and reworded.

• In "Origin and early evolution": "Indeed, the origin of Archaea appears very old indeed..." I am indeed ODing on indeeds.

Not needed, cut.

• In "Classification": "These classification systems aim to organize archaea..."—Current classification systems, perhaps?

Done.

• I don't suppose Tim can make a PNG version of Image:Bacteriorhodopsin.jpg... JPG really doesn't look too good to me. I'd also place the image directly below the table, right-aligned; image staggering isn't set in stone.

Done.

• I'd spotted a somewhat confusing statement regarding phototrophic archaea, but I can't seem to find it now?

It might be the "can capture light but can't do photosynthesis" thing? It's discussed above in Ciar's review. Tim Vickers (talk) 16:00, 28 June 2008 (UTC)

Anyway—excellent work. This FAC is also excellent evidence that articles can indeed benefit from some "de-jargoning" every now and then :) Fvasconcellos (t·c) 15:27, 28 June 2008 (UTC)

• Tentative Support—It is not a light read, but if you can get past the jargon and (in places) dense language it seems like a good article. The reader is probably going to spend a lot of time clicking links in order to understand this fully. But I didn't find any major issues with the presentation.—RJH (talk) 18:40, 28 June 2008 (UTC)

Thanks, Which sections did you feel had dense language? Tim Vickers (talk) 18:43, 28 June 2008 (UTC)

I've gone through again using the readability link above (those are a great addition to the FA process BTW) and straightened out and broken up some knotty sentences See diff. Tim Vickers (talk) 19:13, 28 June 2008 (UTC)

Thank you.—RJH (talk) 14:39, 30 June 2008 (UTC)

• Support - Well written article on a notable and complex topic. The section on metabolism is jargon heavy, but all terms are linked and organic chemistry is very complex (at least it appears that way to me!). I will discussion on comprehensiveness etc. to others. I have made some (very) small changes, I hope these are OK. Once again, well done. -- Mattinbgn\^talk 03:40, 30 June 2008 (UTC)

• One question; is there any reason why the article remains semi-protected? -- Mattinbgn\^talk 03:51, 30 June 2008 (UTC)

As for the jargon, funny you should mention it on the day that Oxidative phosphorylation is on the front page ;-). (But I did find it interesting to read through Wikipedia:Featured article candidates/Oxidative phosphorylation for comparison). Kingdon (talk) 05:16, 30 June 2008 (UTC)

It seems User:Crum375 protected the page because of persistent anon vandalism on 2008-04-04. I do not know why he chose a protection period of three months (especially when you consider that the page never been protected previously). However, since the protection is due to expire in a few days anyway, I had not bothered to unprotect it. --EncycloPetey (talk) 06:31, 30 June 2008 (UTC)

Comments I enjoyed reading this article and can tell you have put a lot of hard work in it. It is the nature of the beast, however, that what follows does not enumerate all the great things you have done. Overall the article becomes far too often a compare and contrast exercise with Bacteria. I would suggest leaving most all the bits that say "similar to bacteria". However with all the pieces that say "Bacteria do/have it this way and Archaea do/have it that way." I would remove the bacteria bit and instead simply say "unique to Archaea". Also this article needs serious work on flow and cohesion with attention to the article as a whole. It seems to have had sections developed more in isolation than not. It is also a little heavy with parenthetical remarks.

• Lead: missing summary of Genetics, Reproduction, and Technology. Too much detail with Carl Woese, 1977 Looking this over again, my biggest issue with the lead is structural.

Carl is only mentioned once and his work is a key event in the history of archaean microbiology, but I cut the date since that isn't critical. I've added some material on genetics and technology.

• Discovery: Not sure if this is the vest heading title. Actually I would put call it "Classifaiction" and have the section already named that tacked on to the end of this one. All this really talks about it is the history of changes made in how these organisms are classified rather than how these organisms were "discovered".

That's debatable, see below for discussion.

• • This powerful approach, known as phylogenetics, is the main method used today The first clause is too peacocky.

Cut "powerful"

• • Archaea were identified as a separate group of prokaryotes in 1977 change identified to classified for better accuracy.

Reworded to "Archaea were first classified as a separate group of prokaryotes in 1977"

• • He later renamed the two groups of prokaryotes Archaea and Bacteria to emphasize this, and argued that together with Eukarya they are three domains of living organisms' A little awkward. Maybe "they compose the the three domains"?

Reworded to "To emphasize this difference, these two domains were later renamed Archaea and Bacteria."

• • This new appreciation of the importance and ubiquity of archaea came mostly from the use of molecular biology techniques to detect prokaryotes in samples of water or soil from their nucleic acids alone. Can we either enumerate these "molecular biology techniques" or link to somewhere that covers these techniques rather than the general field?

Reworded to "This new appreciation of the importance and ubiquity of archaea came from using the polymerase chain reaction to detect prokaryotes in samples of water or soil from their nucleic acids alone."

• • Such techniques eliminate the need to culture organisms in the laboratory, which is often difficult I thin "eliminate the need" is a bit strong, considering in the lead you say this sort of detection is not good enough to properly classify archaea.

Reworded to "This allows the detection and identification of organisms that cannot be cultured in the laboratory, which is often difficult."

• Morphology: Some images of unusual shapes would be better than the chart that does not even specify archaea. Structure here is good

I'm afraid there are very few pictures available under a free license.

• • Individual archaeans range from 0.1 micrometers (μm) to over 15 μm in diameter Is the size range distinct from other single-celled organisims or generally equivalent?

Generally equivalent (although 0.1 um is on the small side) for prokaryotes. I could add "like bacteria" here, but I've been trying to remove these!

• Origin and early evolution: I don't know that anything in this section covers the origin of archaea, nor that the section restricted to talking of early evolution of archaea. Lack of structure is now biggest concern.

Title renamed to "origin and evolution", since the point where the archaea originated was when they diverged from other forms of life.

• Classification: I would merge this with first section as I stated above. I still think the discussion of the classification of archaea as a domain and the classification within that domain should group together in some way. At least as sub-heading under a larger "Classification" section.

See bottom of this review for discussion of this point. Tim Vickers (talk) 04:03, 2 July 2008 (UTC)

• • populations of archaea show clusters of related cells that can be seen as species and the argument that these species are points within an interconnected net of gene transfer events What this debate is actually about is incomprehensible to me.

Simplified and clarified.

Better, but I still wonder if "groups" can be clarified. They aren't completely arbitrary are they?

That depends on who you ask, some argue that they are indeed arbitrary! This is at best a statistical definition of species. I've tried being a bit more specific on how these groups are being defined. - "The area is contentious; with, for example, some data suggesting that in archaea such as the genus Ferroplasma, individual cells can be grouped into populations that have highly-similar genomes and rarely transfer genes with more divergent groups of cells. These groups of cells are argued to be analogous to species."

• Cell structure: This is the first section with any noticeable attempt organization of the writing. Although why cell walls are more distinct from cell membranes than flagella is lost to me. Bullets points really should be avoided when you get to multiple sentences.

Rearranged into paragraphs

• • Archaea are similar to bacteria in many aspects of their cell structure, but other characteristics set the archaea apart. This has no meaning

Reworded to "Archaea are similar to bacteria in their general cell structure, but the composition and organization of some of these structures set the archaea apart."

• • These molecules resemble soap molecules Why do you expect soap molecules to be a touch point for readers?

Analogy removed.

• • (the phosphate "head", shown as green circles, labeled 4 and 8, in the Figure) Direct references to figure in the text body rather than the caption. Yuck!

This was added in response to the review by Awadewit above. :) I've removed it again.

• • This double sheet of phospholipids is the major structure in cell membranes You lost me right here. How do two phosopholipids become a "sheet"? How is this configured with the life inside and the world outside? Water is likely to be on both sides. There are other structures to cell membranes other than a layer of goo keeping the life inside and the world outside?

Reworded, but this isn't the place for discussing membrane structure in detail. Hopefully the new wording should be a better summary of the article on cell membranes.

• • Ether bonds are more chemically-resistant then ester bonds and the downside/trade-off to ether bonds is?

I haven't seen any discussion of a downside, so I can't really speculate on that point.

• • These branched chains may help prevent archaean membranes from becoming leaky at high temperatures. and the downside/trade-off is?

Ditto, I don't think that is known.

• • In some archaea the typical phospholipid bilayer (labeled 9 at the right) is replaced by a single monolayer (labeled 10 at the right) Well the caption says 9 is bacteria/eukaryote model and 10 an archaea.

Removed and reworded. Poor usage of the word "typical", reworded to "in some archaea the phospholipid bilayer is replaced by a single monolayer."

• • bacteria possessing cell walls made from peptidoglycan . . . this polymer differs from the peptidoglycan of bacteria since it lacks D-amino acids and N-acetylmuramic acid I followed the S-layer/chain mail description nicely. This peptidoglycan/pseudopeptodoglycan bit however lost me. What is it besides hard to spell?

Not particularly important is what it is, I've cut this sentence.

• • while they are similar to bacterial flagella in that they are rotatory motors driven by a proton gradient or you could they are similar in operation (and then either offer the details or not).

Question - I'm sorry, I'm not sure I understand this comment. Are you wanting more details on how the flagella operate?

I intended to point out that you could say this in more common terms like "they are similar in operation", rather than describing how they operate in a techincal way that some readers might not comprehend. The parenthetical is intended to say I don't have strong feels on including the details or not once a more comprehenable term like "operation" is in there.--BirgitteSB 19:08, 1 July 2008 (UTC)

Reworded and expanded to "Archaea also have flagella, and these operate in a similar way to bacterial flagella - they are stiff stalks that are driven by rotatory motors at the base of the flagella. These motors are powered by the proton gradient across the membrane. "

• • The bacterial flagellum is a modified type III secretion system, while archaeal flagella appear to have evolved from to the bacterial type IV pili. This could be explained in more meaningful terms.

Reworded to "The two types of flagella evolved from different ancestors, the bacterial flagellum evolved from a type III secretion system, while archaeal flagella appear to have evolved from the bacterial type IV pil"

• • In contrast to the bacterial flagellum, where filament proteins move up a central pore and are added to the tip of the filament, archaeal filaments appear to be synthesized by adding subunits to their base. That is a little hard to grasp, can it link somewhere or be explained in detail.

Reworded to "In contrast to the bacterial flagellum, which is a hollow stalk and is assembled by subunits moving up the central pore and then adding onto the tip of the flagella, archaeal flagella are synthesized by adding subunits onto their base."

• Metabolism: This is the weakest section so far. Intro paragraph skips over Hererortrophs. How exactly is that image relevant to this section?
  • Archaea exhibit a variety of different types of metabolism, obtaining the energy they need from many different chemical reactions As do all organisms; lacks meaning.

Not really, most eukaryotes use a very limited set of nutrients. Reworded to "Archaea exhibit a great variety of chemical reactions in their metabolism and use many different sources of energy."

• • with archaea that grow on complex organic compounds (the chemoorganotrophs) Kill the parenthetical and just stick with three basic groups. It just is a confusing new term never used again and adds nothing important.

Cut and reworded.

• • These similarities with other organisms probably reflect the early evolution of carbohydrate metabolism in the history of life Or else this could reflect that there are limited options for metabolizing carbohydrates efficiently

Good point, added.

• • A common reaction in [methogens] . . . I don't understand why the details of this chemical reaction should be included.

Question - Do you think it would be better with more equations, or better without this equation?

Actually I was going for a different angle. If this chemistry is a significant point about Archaea, explain the significance explicitly and keep it. If it not or if other other chemistry has equal significance, cut it or add the others. I don't have a strong feeling about equations per se.--BirgitteSB 19:08, 1 July 2008 (UTC)

It's an important reaction to methanogens, but no more important to the archaea in general than sulfur reduction or ammonia oxidation. I've removed it.

• • Methanogenesis involves a range of unique coenzymes, such as coenzyme M and methanofuran Unique to Archaea or to methogens. (I feel the article is losing its focus about now)

Reworded to "Methanogenesis involves a range of coenzymes that are unique to these archaea"

• Genetics:
  • Archaeal plasmids are increasingly important as genetic tools and allow the performance of genetic studies in archaea. This has lost me and it has no links.

Cut.

• • As with the bacteriophages that infect bacteria, some viruses replicate within archaea Or as with all types of living organisms, archara can be infected with viruses. Similarity to bacteria is only worth noting when it is similarity to bacteria alone (or nearly so).

Good point. Reworded to "Archaea can be infected by viruses."

• • Archaea are genetically distinct from other organisms As are Bacteria, Jellyfish, Giraffes, and BirgitteSB. That doesn't mean much.

Reworded to "Archaea are genetically distinct from bacteria and eukaryotes"

• • Transcription and translation in archaea are more similar to those in eukaryotes than in bacteria, with archaean RNA polymerase II and ribosomes being very similar to their equivalents in eukaryotes.[77] The archaeal RNA polymerase in transcription also seems to function in a similar way to that of eukaryotes Can you not say "similar . . . to eukaryotes" so often in succession?

Cut and reworded. "Transcription and translation in archaea are more similar to these processes in eukaryotes than in bacteria, with archaean RNA polymerase II and ribosomes being very close to their equivalents in eukaryotes. The archaeal RNA polymerase in transcription also seems to function like that of eukaryotes, with similar assemblies of proteins (the general transcription factors) directing the binding of the RNA polymerase to a gene's promoter. However, other archaean transcription factors are closer to those found in bacteria."

• Reproduction:
  • (they have the same karyotype) Kayotype begins "A karyotype is the characteristic chromosome complement of a eukaryote species" One of these articles is wrong.

Reworded to "these will all have the same genetic material", they only have one chromosome anyway.

• • a complex cell cycle; after the cell's chromosome is replicated and the two daughter chromosomes are separated, the cell divides Seems simple compared to meiosis; what's so complex?

True, "complex" has no real meaning here. Reworded to "Cell division is controlled in the archaea in a cell cycle"

• • Spores, such as the endospores made by some bacteria, are not formed in any of the known archaea Many things are not formed in archaea, why does this merit inclusion?

Since this is defining characteristic that separates them from both bacteria and eukaryotes. I've reworded this to "Spores are made by both bacteria and eukaryotes, but are not formed in any of the known archaea."

• • Some species of Haloarchaea undergo phenotypic switching and grow as several different types of cell, including thick-walled structures that are resistant to osmotic shock and allow the archaea to survive in water at low concentrations of salt, but these are not reproductive structures and may instead help them disperse to new habitats Maybe this should be in "cell structure" not "Reproduction".

No, this is the closest they get to spores, so I think this belongs best here.

• Ecology: You might want to particularly mention plankton here. Or else take out the image and the mention in the lead. You also might want to move "Interaction with other organisms" before "Role in chemical cycling" so you can explains termites/ruminants and methogens before mentioning them as in aside in the role on global warming.

Added plankton in text. The section on cycling fits well with the habitats section, so I've just removed the mention of termites in this section.

• • the formate-consuming methanogen What does formate-consuming signify?

Not much, cut. Tim Vickers (talk) 17:47, 1 July 2008 (UTC)

Hope that helps --BirgitteSB 04:48, 1 July 2008 (UTC)

• • • I'll try to begin implementing some of these suggestions tomorrow (It's rather late for me locally). I do want to point out two specfic points in your comments that either perhaps should not be made. First, the statements where the text says "Bacteria have"/"Archaea have" cannot be changed to "Unique to archaea" in most cases. Remember that there is a third group, the eukaryotes, and in many of these situations where the comparison was made, archaea actually share their trait with eukaryotes. In other words, revising those passages will be a bit trickier, though some may be changeable.
    • Second, it is not correct to replace "...were identified" with "...were classified". Those two statements mean entirely different things. Identification is the recognition or discovery of a group; classification is the formal publication of a scientific name and description that places a group in context. The archaea were identified in 1977 as a new group, but were still classified alongside the bacteria as a kingdom. It was not until 1990 that the group was classified as a separate domain. Related to this, the two sections you've identified as pertaining to classification really do separate things. The "Discovery" section discusses the separateness of the group and its recognition as separate, so it treats the group as a cohesive whole distinct from other groups. By contrast, the "Classification" section discusses relationships within the group between different members, treating the members as units of a diverse assemblage. I fear that merging the two sections would blur this important difference in the focus of the two sections. The "Discovery" really has more in common with the "Origin and early evolution section" than with the "Classification" section. There is also the problem that the "Discovery" section is a general read, that introduces what the group is and something of its importance; it must therefore appear early in the article. The "Classification" section covers material that is more specialized, and much harder to explain to the layman, so placing it early in the article may befuddle some readers. I'm not sure that the two sections can be neatly joined because of this. --EncycloPetey (talk) 05:29, 1 July 2008 (UTC)
      • First: Perhaps then compare them to eukaruote where they are not unique. Bacteria has 16 instances of the word archaea. This article use "bacteria" 50 times, and I didn't even count things like cyanobacteria.
        • I agree. --EncycloPetey (talk) 15:56, 1 July 2008 (UTC)
      • Second: I am not sure when a few species among a selection of birds that were always regarded as one genus are assigned a brand new genus all there own, that those birds aren't considered to be "discoverd" at that point. But if I am wrong about this maybe you can clarify why in the article a little more so other can't think along the same lines.--BirgitteSB 12:09, 1 July 2008 (UTC)
        • Thank you for clarifying your concern; obviously the article isn't making that (second) point clear. Birds are probably not a good analogy for this situation, nor is a discussion at the level of genus. Imagine rather that you suddenly discover that some of those lights in the sky are actually planets like Earth, or that you suddenly realize that some of the "rocks" around you are actually living things. This would be closer to the magnitutde of Woese's discovery, as it marked a major shift in thinking about life on Earth. What happened in the case of the Archaea was that a few species were known to exist and had previously been classified among bacteria because they were tiny and nucleus-free. Carl Woese discovered the distinctiveness of those few known species, and along with this recognition came the discovery of dozens, then hundreds, of new organisms previously unknown to exist. Even now, microbiologists will take a random sample from a random location and "shotgun" for possible DNA. This often leads to the discovery of new Archaea, which turn out to be ubiquitous on Earth. I guess another analogy would be if we had only ever seen penguins and ostriches, then someone suddenly thought to look upwards and discovered there were birds flying around in the sky. If the enormity of the discovery hasn't been made clear in the article, then we should certainly clarify this point. --EncycloPetey (talk) 15:55, 1 July 2008 (UTC)

Thank you, Birgitte, a characteristically thorough review! Tim Vickers (talk) 13:54, 1 July 2008 (UTC)

I've changed the order of the sections, what do you think of the new arrangement? Tim Vickers (talk) 04:02, 2 July 2008 (UTC)

The above discussion is preserved as an archive. Please do not modify it. No further edits should be made to this page.

References